Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z A a (cosmolkit.BioCrystalCell attribute) A (cosmolkit.ResidueCode attribute) A2G (cosmolkit.ResidueCode attribute) AA (cosmolkit.ResidueInfoKind attribute) AAD (cosmolkit.ResidueInfoKind attribute) ABA (cosmolkit.ResidueCode attribute) Absolute (cosmolkit.StereoGroupKind attribute) AC (cosmolkit.Element attribute) ACA (cosmolkit.ResidueCode attribute) AccessDenied (cosmolkit.OperationErrorKind attribute) accession_code (cosmolkit.BioEntityDbRef attribute) accession_index (cosmolkit.BioSiftsUnpResidue attribute) ACE (cosmolkit.ResidueCode attribute) ACN (cosmolkit.ResidueCode attribute) ACT (cosmolkit.ResidueCode attribute) action (cosmolkit.OperationError property) ACTIVE (cosmolkit.LayeredFingerprintLayers attribute) ActiveAtomOutOfRange (cosmolkit.MatrixErrorKind attribute) ActiveBondEndpointMissing (cosmolkit.MatrixErrorKind attribute) ActiveBondOutOfRange (cosmolkit.MatrixErrorKind attribute) ActiveBondsWithoutAtoms (cosmolkit.MatrixErrorKind attribute) actual (cosmolkit.AdjustHsError property) (cosmolkit.AromaticityError property) (cosmolkit.AtropisomerError property) (cosmolkit.AttachmentExpansionError property) (cosmolkit.BoundsMatrixError property) (cosmolkit.CanonicalRankError property) (cosmolkit.CipRankError property) (cosmolkit.ConjugationError property) (cosmolkit.CoordinateInputError property) (cosmolkit.CxQueryLoweringError property) (cosmolkit.CxStereoGroupMergeError property) (cosmolkit.DescriptorError property) (cosmolkit.DoubleBondStereoError property) (cosmolkit.DrawingError property) (cosmolkit.FingerprintBatchError property) (cosmolkit.ForceFieldError property) (cosmolkit.FragmentCoordinateViewError property) (cosmolkit.FullCopyComponentError property) (cosmolkit.HybridizationError property) (cosmolkit.HydrogenError property) (cosmolkit.KekulizeError property) (cosmolkit.MappingValidationError property) (cosmolkit.MmffForceFieldError property) (cosmolkit.MmjsonStructureError property) (cosmolkit.MoleculeHashError property) (cosmolkit.MoleculeTransferError property) (cosmolkit.OperationError property) (cosmolkit.PathError property) (cosmolkit.PdbStructureFinalizationError attribute) (cosmolkit.PickleError property) (cosmolkit.PotentialStereoError property) (cosmolkit.PropertyValueError property) (cosmolkit.QueryMatchContextError property) (cosmolkit.QueryStateError property) (cosmolkit.ReactionRunError property) (cosmolkit.ReactionWriteError property) (cosmolkit.ScaffoldError property) (cosmolkit.SdfError property) (cosmolkit.SdfReadError property) (cosmolkit.SmartsWriteError property) (cosmolkit.SmilesStereoError property) (cosmolkit.StereoError property) (cosmolkit.StereoOrderError property) (cosmolkit.TautomerRunError property) (cosmolkit.TopologicalTorsionPathScoreError property) (cosmolkit.TopologyEditError property) (cosmolkit.TransformError property) (cosmolkit.UffBoundsCause attribute) (cosmolkit.UffBuilderError property) (cosmolkit.UffTorsionBondQueryError property) (cosmolkit.UffTypingError property) (cosmolkit.XmlParseError property) actual_atoms (cosmolkit.CanonicalRankError property) actual_bonds (cosmolkit.CanonicalRankError property) actual_degree (cosmolkit.UffBuilderError property) actual_rows (cosmolkit.DescriptorError property) (cosmolkit.HydrogenError property) actual_start (cosmolkit.BioStructureError property) ACY (cosmolkit.ResidueCode attribute) add_2d_conformer() (cosmolkit.MoleculeBuilder method) add_2d_coordinates_() (cosmolkit.Molecule method) add_2d_coordinates_with_params_() (cosmolkit.Molecule method) add_3d_conformer() (cosmolkit.MoleculeBuilder method) add_3d_conformer_() (cosmolkit.Molecule method) add_3d_conformer_with_params_() (cosmolkit.Molecule method) add_angle_constraint_() (cosmolkit.MolecularForceField method) add_atom() (cosmolkit.MoleculeBuilder method) add_bond() (cosmolkit.MoleculeBuilder method) add_coords (cosmolkit.AddHsParams attribute) add_distance_constraint_() (cosmolkit.MolecularForceField method) add_hydrogens_() (cosmolkit.Molecule method) add_hydrogens_with_params_() (cosmolkit.Molecule method) add_position_constraint_() (cosmolkit.MolecularForceField method) add_residue_info (cosmolkit.AddHsParams attribute) add_stereo_group() (cosmolkit.MoleculeBuilder method) add_substance_group() (cosmolkit.MoleculeBuilder method) add_torsion_constraint_() (cosmolkit.MolecularForceField method) added (cosmolkit.SearchMcsError property) AddedAtomRow (cosmolkit.FullCopyComponentErrorKind attribute) AddHsParams (class in cosmolkit) addition (cosmolkit.HydrogenError property) additional_output (cosmolkit.BatchFingerprintOutput attribute) address (cosmolkit.MmcifSheetError property) AddrInUse (cosmolkit.IoErrorKind attribute) AddrNotAvailable (cosmolkit.IoErrorKind attribute) AddsProductAtom (cosmolkit.ReactionApplyErrorKind attribute) adjacency (cosmolkit.ReactionProductError property) Adjacency (cosmolkit.ReactionProductErrorKind attribute) adjacency (cosmolkit.RingFindingError property) Adjacency (cosmolkit.RingFindingErrorKind attribute) AdjacencyAtomOutOfRange (cosmolkit.ValenceErrorKind attribute) AdjacencyBondOutOfRange (cosmolkit.ValenceErrorKind attribute) AdjacencyEndpointMismatch (cosmolkit.ValenceErrorKind attribute) AdjacencyError AdjacencyErrorKind (class in cosmolkit) AdjacencyMismatch (cosmolkit.QueryGraphErrorKind attribute) (cosmolkit.TopologyValidationErrorKind attribute) ADJUST_HS (cosmolkit.SanitizeOperations attribute) AdjustHs (cosmolkit.SanitizeErrorKind attribute) (cosmolkit.SanitizeStage attribute) AdjustHsError AdjustHsErrorKind (class in cosmolkit) ADP (cosmolkit.ResidueCode attribute) after (cosmolkit.KekulizeError property) AG (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) Agent (cosmolkit.ReactionRole attribute) agent_template() (cosmolkit.Reaction method) agent_templates (cosmolkit.Reaction attribute) AgentFragments (cosmolkit.ReactionParseErrorKind attribute) AGM (cosmolkit.ResidueCode attribute) AIB (cosmolkit.ResidueCode attribute) aid2 (cosmolkit.CrystalffTorsionPreferencesError property) aid3 (cosmolkit.CrystalffTorsionPreferencesError property) AL (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) ALA (cosmolkit.ResidueCode attribute) ALC (cosmolkit.ResidueCode attribute) Algorithm (cosmolkit.DescriptorReadErrorKind attribute) (cosmolkit.OperationErrorKind attribute) align_conformers_() (cosmolkit.Molecule method) align_conformers_with_params_() (cosmolkit.Molecule method) align_loops (cosmolkit.BioMmcifWriteParams attribute) align_pairs (cosmolkit.BioMmcifWriteParams attribute) align_to_() (cosmolkit.Molecule method) align_to_with_params_() (cosmolkit.Molecule method) alignment (cosmolkit.OperationError property) Alignment (cosmolkit.OperationErrorKind attribute) alignment_transform_to() (cosmolkit.Molecule method) alignment_transform_to_with_params() (cosmolkit.Molecule method) AlignmentAtomMap (class in cosmolkit) AlignmentError AlignmentErrorKind (class in cosmolkit) AlignmentParameters (class in cosmolkit) AlignmentResult (class in cosmolkit) AlignmentTransform (class in cosmolkit) ALL (cosmolkit.CxSmilesFields attribute) (cosmolkit.SanitizeOperations attribute) all_bonds_explicit (cosmolkit.RandomSmilesWriteParams attribute) (cosmolkit.SmilesWriteParams attribute) ALL_BUT_COORDS (cosmolkit.CxSmilesFields attribute) all_conformer_best_rmsds() (cosmolkit.Molecule method) all_conformer_best_rmsds_with_params() (cosmolkit.Molecule method) all_conformers (cosmolkit.PdbWriteParams attribute) ALL_FEATURES (cosmolkit.AvalonFingerprintFlags attribute) all_hydrogens_explicit (cosmolkit.RandomSmilesWriteParams attribute) (cosmolkit.SmilesWriteParams attribute) ALL_SOURCE_BITS (cosmolkit.LayeredFingerprintLayers attribute) AllConformerRmsdParameters (class in cosmolkit) Allene (cosmolkit.ChiralTag attribute) allocate_atom_counts() (cosmolkit.FingerprintAdditionalOutput method) allocate_atom_to_bits() (cosmolkit.FingerprintAdditionalOutput method) allocate_atoms_per_bit() (cosmolkit.FingerprintAdditionalOutput method) allocate_bit_info_map() (cosmolkit.FingerprintAdditionalOutput method) allocate_bit_paths() (cosmolkit.FingerprintAdditionalOutput method) Allocation (cosmolkit.UnsignedStreamArrayErrorKind attribute) AllocationFailed (cosmolkit.BoundsMatrixErrorKind attribute) (cosmolkit.InchiErrorKind attribute) allow_cxsmiles (cosmolkit.ReactionParseParams attribute) (cosmolkit.SmartsParseParams attribute) (cosmolkit.SmilesParseParams attribute) allow_nontetrahedral (cosmolkit.PotentialStereoParams attribute) alpha (cosmolkit.BioCrystalCell attribute) AlreadyExists (cosmolkit.IoErrorKind attribute) altloc (cosmolkit.AtomAddress attribute) (cosmolkit.BioAtom attribute) (cosmolkit.BioAtomRow attribute) (cosmolkit.ProteinAtomRef attribute) AltLocLabel (class in cosmolkit) AltLocRequest (class in cosmolkit) ALY (cosmolkit.ResidueCode attribute) AM (cosmolkit.Element attribute) AmbiguousCoordinates (cosmolkit.MolWriteErrorKind attribute) (cosmolkit.PdbWriteErrorKind attribute) AmbiguousCoordinateSelection (cosmolkit.SmilesParseErrorKind attribute) AminoAcid (cosmolkit.ResidueKind attribute) And (cosmolkit.StereoGroupKind attribute) angle (cosmolkit.MmffParamError property) Angle (cosmolkit.MmffParamErrorKind attribute) (cosmolkit.MmffParamTable attribute) AngleBadOrder (cosmolkit.ForceFieldKernelErrorKind attribute) AngleBoundsOrder (cosmolkit.ForceFieldKernelErrorKind attribute) AngleDegeneratePoints (cosmolkit.ForceFieldKernelErrorKind attribute) AngleIndexOutOfRange (cosmolkit.ForceFieldKernelErrorKind attribute) AngleOutOfRange (cosmolkit.ForceFieldKernelErrorKind attribute) aniso_b (cosmolkit.BioRefinementInfo attribute) AnisotropicU (cosmolkit.BioMmcifReadStage attribute) anisou (cosmolkit.BioAtom attribute) (cosmolkit.BioAtomRow attribute) AnisouIntegerOutsideSourceIntRange (cosmolkit.PdbModelTransitionErrorKind attribute) AnisouWithoutAtom (cosmolkit.PdbModelTransitionErrorKind attribute) Annotation (cosmolkit.ReactionValidationErrorKind attribute) Any (cosmolkit.AtomQueryPredicateKind attribute) (cosmolkit.BioAsu attribute) (cosmolkit.BondQueryPredicateKind attribute) (cosmolkit.BondStereo attribute) (cosmolkit.McsAtomComparator attribute) (cosmolkit.McsBondComparator attribute) any() (cosmolkit.AltLocRequest static method) AnyHeavyAtom (cosmolkit.McsAtomComparator attribute) AnyPolymer (cosmolkit.SubstanceGroupKind attribute) AppendedRow (cosmolkit.QueryStateErrorKind attribute) AppendedRowCount (cosmolkit.QueryStateErrorKind attribute) ApplicabilityArity (cosmolkit.ReactionApplyErrorKind attribute) apply_reaction() (cosmolkit.Molecule method) apply_reaction_() (cosmolkit.Molecule method) apply_reaction_with_params() (cosmolkit.Molecule method) apply_reaction_with_params_() (cosmolkit.Molecule method) approx() (cosmolkit.BioTransform method) AR (cosmolkit.Element attribute) ARG (cosmolkit.ResidueCode attribute) argument (cosmolkit.ForceFieldKernelError property) (cosmolkit.JsonError property) (cosmolkit.UffInversionContributionError property) ArgumentListTooLong (cosmolkit.IoErrorKind attribute) aromatic (cosmolkit.AtomQueryPredicate attribute) AROMATIC (cosmolkit.BondOrder attribute) Aromatic (cosmolkit.BondOrder attribute) aromatic_matches_conjugated (cosmolkit.SubstructMatchParams attribute) aromatic_matches_single_or_double (cosmolkit.SubstructMatchParams attribute) AromaticAtomOutsideRing (cosmolkit.KekulizeErrorKind attribute) aromaticity (cosmolkit.ConjugationError property) Aromaticity (cosmolkit.ConjugationErrorKind attribute) AROMATICITY (cosmolkit.LayeredFingerprintLayers attribute) aromaticity (cosmolkit.MmffMolPropertiesError property) Aromaticity (cosmolkit.MmffMolPropertiesErrorKind attribute) aromaticity (cosmolkit.OperationError property) Aromaticity (cosmolkit.OperationErrorKind attribute) (cosmolkit.SanitizeErrorKind attribute) AromaticityError AromaticityErrorKind (class in cosmolkit) AromaticityModel (class in cosmolkit) AromaticityParams (class in cosmolkit) AromaticRingCountOutOfRange (cosmolkit.AromaticityErrorKind attribute) Array (cosmolkit.MmjsonUnexpectedType attribute) ArrayLength (cosmolkit.MmjsonStructureErrorKind attribute) AS (cosmolkit.Element attribute) as_bio_structure() (cosmolkit.Protein method) as_bool() (cosmolkit.PropertyValue method) as_bytes() (cosmolkit.AtomName method) (cosmolkit.FromUtf8Error method) as_double() (cosmolkit.PropertyValue method) as_int() (cosmolkit.PropertyValue method) as_int_vector() (cosmolkit.PropertyValue method) as_str() (cosmolkit.AtomName method) (cosmolkit.CipDescriptor method) as_string() (cosmolkit.PropertyValue method) as_u16() (cosmolkit.ResidueCode method) as_uint() (cosmolkit.PropertyValue method) asa (cosmolkit.LabuteAsaContributions attribute) ASN (cosmolkit.ResidueCode attribute) ASP (cosmolkit.ResidueCode attribute) Assemblies (cosmolkit.BioMmcifReadStage attribute) assemblies (cosmolkit.BioStructure attribute) (cosmolkit.BioStructureParts attribute) assembly (cosmolkit.BioMmcifWriteParams attribute) assign_aromaticity_() (cosmolkit.Molecule method) assign_aromaticity_with_params_() (cosmolkit.Molecule method) assign_chiral_tags_from_structure_() (cosmolkit.Molecule method) assign_chiral_tags_from_structure_with_params_() (cosmolkit.Molecule method) assign_cip_labels_() (cosmolkit.Molecule method) assign_cip_labels_with_options_() (cosmolkit.Molecule method) assign_radicals_() (cosmolkit.Molecule method) assign_ring_families_() (cosmolkit.Molecule method) assign_ring_families_with_params_() (cosmolkit.Molecule method) assign_rings_() (cosmolkit.Molecule method) assign_valence_() (cosmolkit.Molecule method) assign_valence_with_params_() (cosmolkit.Molecule method) assignment (cosmolkit.SmilesStereoError property) Assignment (cosmolkit.SmilesStereoErrorKind attribute) AssignmentBondOutOfRange (cosmolkit.AtropisomerErrorKind attribute) AssignmentLength (cosmolkit.UffBoundsCauseKind attribute) asu (cosmolkit.BioConnection attribute) ASX (cosmolkit.ResidueCode attribute) asym_id (cosmolkit.MmcifSiftsUnpError property) AsymId (cosmolkit.AtomSiteIdentityField attribute) AT (cosmolkit.Element attribute) Atom (class in cosmolkit) atom (cosmolkit.AdjacencyError property) (cosmolkit.AdjustHsError property) (cosmolkit.AromaticityError property) (cosmolkit.AtropisomerError property) Atom (cosmolkit.ChemCompModelErrorKind attribute) atom (cosmolkit.CipLabelerError property) (cosmolkit.CipRankError property) (cosmolkit.ConjugationError property) (cosmolkit.Coordinate2DLayoutError property) (cosmolkit.CoordinateValidationError property) (cosmolkit.CxQueryLoweringError property) (cosmolkit.DoubleBondStereoError property) (cosmolkit.EnumerationError property) (cosmolkit.HybridizationError property) (cosmolkit.HydrogenError property) (cosmolkit.KekulizeError property) (cosmolkit.MatrixError property) (cosmolkit.MolPostError property) (cosmolkit.OperationError property) (cosmolkit.PathError property) (cosmolkit.PotentialStereoError property) (cosmolkit.QueryAtomConversionError property) (cosmolkit.QueryGraphError property) (cosmolkit.QueryMatchContextError property) (cosmolkit.QueryStateError property) (cosmolkit.RadicalError property) (cosmolkit.ReactionApplyError property) (cosmolkit.ReactionParseError property) (cosmolkit.ReactionProductError property) (cosmolkit.ReactionRunError property) (cosmolkit.ReactionValidationError property) (cosmolkit.ReactionValidationIssue attribute) (cosmolkit.RingFindingError property) (cosmolkit.RingStereoRelation attribute) (cosmolkit.ScaffoldError property) Atom (cosmolkit.SdfPropertyListTarget attribute) atom (cosmolkit.SdfWriteError property) Atom (cosmolkit.SdfWriteErrorKind attribute) atom (cosmolkit.SearchMcsError property) (cosmolkit.SelectedBondCopyError property) (cosmolkit.SelectedSubstanceGroupCopyError property) (cosmolkit.SmartsParseError property) (cosmolkit.SmartsWriteError property) (cosmolkit.SmilesParseError property) Atom (cosmolkit.SmilesParseErrorKind attribute) atom (cosmolkit.StereoError property) (cosmolkit.StereoOrderError property) (cosmolkit.StereoReadError property) (cosmolkit.TautomerRunError property) (cosmolkit.TopologyEditError property) (cosmolkit.TopologyValidationError property) (cosmolkit.TransformError property) (cosmolkit.ValenceError property) (cosmolkit.WedgeError property) atom() (cosmolkit.BioStructure method) Atom() (cosmolkit.LigandRef static method) atom() (cosmolkit.Molecule method) (cosmolkit.TautomerMoleculeView method) atom_bits (cosmolkit.TopologicalFingerprintOutput attribute) (cosmolkit.TopologicalFingerprintOutputRequest attribute) (cosmolkit.TopologicalFingerprintResult attribute) atom_by_altloc() (cosmolkit.BioStructure method) ATOM_CLASS_PATH (cosmolkit.AvalonFingerprintFlags attribute) atom_code (cosmolkit.OperationError property) atom_comparator (cosmolkit.McsParameters attribute) atom_compare_parameters (cosmolkit.McsParameters attribute) atom_contributions (cosmolkit.LabuteAsaContributions attribute) atom_count (cosmolkit.AdjacencyError property) (cosmolkit.AlignmentError property) (cosmolkit.AromaticityError property) (cosmolkit.AtropisomerError property) ATOM_COUNT (cosmolkit.AvalonFingerprintFlags attribute) atom_count (cosmolkit.BioStructureError property) (cosmolkit.CanonicalRankError property) (cosmolkit.CipLabelerError property) (cosmolkit.CipRankError property) (cosmolkit.ConjugationError property) (cosmolkit.Coordinate2DLayoutError property) (cosmolkit.CoordinateValidationError property) (cosmolkit.DoubleBondStereoError property) (cosmolkit.DrawingError property) (cosmolkit.FragmentWriteInputError property) (cosmolkit.GenerationError property) (cosmolkit.HydrogenError property) (cosmolkit.KekulizeError property) (cosmolkit.MatrixError property) (cosmolkit.McsResult attribute) (cosmolkit.MoleculeHashError property) (cosmolkit.NonbondedFragmentMappingError property) (cosmolkit.OperationError property) (cosmolkit.PathError property) (cosmolkit.PotentialStereoError property) (cosmolkit.QueryGraphError property) (cosmolkit.ReactionParseError property) (cosmolkit.ReactionRunError property) (cosmolkit.ReactionValidationError property) (cosmolkit.RingFindingError property) (cosmolkit.SelectedSubstanceGroupCopyError property) (cosmolkit.SmartsWriteError property) (cosmolkit.SmilesParseError property) (cosmolkit.StereoError property) (cosmolkit.StereoOrderError property) (cosmolkit.SubstructMatchError property) (cosmolkit.TautomerRunError property) (cosmolkit.TemplateAttachmentOrderError property) (cosmolkit.TopologicalTorsionPathScoreError property) (cosmolkit.TopologyEditError property) (cosmolkit.TopologyValidationError property) (cosmolkit.TransformError property) (cosmolkit.UffTypingError property) (cosmolkit.ValenceError property) atom_counts (cosmolkit.BatchFingerprintAdditionalOutput attribute) (cosmolkit.FingerprintAdditionalOutput attribute) (cosmolkit.LayeredFingerprintParams attribute) (cosmolkit.LayeredFingerprintResult attribute) atom_degree() (cosmolkit.TautomerMoleculeView method) atom_fields (cosmolkit.PdbReaderCause property) atom_id (cosmolkit.LigandRef attribute) (cosmolkit.UffBuilderError property) (cosmolkit.UffTypingError property) atom_index (cosmolkit.AtomPairError property) (cosmolkit.CanonicalRankError property) (cosmolkit.ForceFieldError property) (cosmolkit.FragmentWriteInputError property) (cosmolkit.GenerationError property) (cosmolkit.MmffForceFieldError property) (cosmolkit.MmffMolPropertiesError property) (cosmolkit.NonbondedFragmentMappingError property) (cosmolkit.SmilesParseError property) (cosmolkit.UffBuilderError property) (cosmolkit.UffTypingError property) atom_indices (cosmolkit.ConformerAlignmentParameters attribute) atom_invariants (cosmolkit.TopologicalFingerprintParams attribute) atom_invariants_generator (cosmolkit.AtomPairFingerprintParams attribute) (cosmolkit.TopologicalTorsionFingerprintParams attribute) ATOM_LABELS (cosmolkit.CxSmilesFields attribute) atom_map (cosmolkit.AlignmentParameters attribute) (cosmolkit.AlignmentResult attribute) (cosmolkit.Atom attribute) (cosmolkit.MoleculeAtom attribute) (cosmolkit.QueryAtom attribute) atom_mapping (cosmolkit.MatchResult attribute) atom_maps (cosmolkit.AllConformerRmsdParameters attribute) (cosmolkit.BestAlignmentParameters attribute) (cosmolkit.CoordinateRmsdParameters attribute) atom_match (cosmolkit.SubstructMatchParams attribute) atom_metadata() (cosmolkit.Molecule method) (cosmolkit.TautomerMoleculeView method) atom_name (cosmolkit.PdbSsbondResolutionError property) ATOM_OCTAHEDRAL (cosmolkit.PotentialStereoType attribute) atom_order (cosmolkit.CompiledQuery attribute) atom_pair() (cosmolkit.MorganAtomInvariantsGenerator static method) atom_pairs() (cosmolkit.MatchResult method) atom_position() (cosmolkit.BioStructure method) atom_properties (cosmolkit.SubstructMatchParams attribute) atom_property (cosmolkit.EnumerationError property) (cosmolkit.LegacyStereoError property) (cosmolkit.OperationError property) (cosmolkit.ReactionProductError property) (cosmolkit.ScaffoldError property) (cosmolkit.TautomerRunError property) atom_property_bool() (cosmolkit.Molecule method) atom_property_double() (cosmolkit.Molecule method) atom_property_int() (cosmolkit.Molecule method) atom_property_int_vector() (cosmolkit.Molecule method) atom_property_string() (cosmolkit.Molecule method) atom_property_string_vector() (cosmolkit.Molecule method) atom_property_uint() (cosmolkit.Molecule method) ATOM_PROPS (cosmolkit.CxSmilesFields attribute) atom_ranks (cosmolkit.PotentialStereoResult attribute) atom_rings (cosmolkit.RingSearchResult attribute) atom_rows (cosmolkit.AromaticityError property) atom_span (cosmolkit.BioResidue attribute) (cosmolkit.BioResidueRow attribute) ATOM_SQUAREPLANAR (cosmolkit.PotentialStereoType attribute) atom_state (cosmolkit.SdfWriteError property) ATOM_SYMBOL_PATH (cosmolkit.AvalonFingerprintFlags attribute) atom_symbols (cosmolkit.FragmentCxSmilesWriteParams attribute) (cosmolkit.FragmentSmilesWriteParams attribute) ATOM_TETRAHEDRAL (cosmolkit.PotentialStereoType attribute) atom_to_bits (cosmolkit.BatchFingerprintAdditionalOutput attribute) (cosmolkit.FingerprintAdditionalOutput attribute) ATOM_TRIGONALBIPYRAMIDAL (cosmolkit.PotentialStereoType attribute) atom_type (cosmolkit.BioMmcifWriteParams attribute) ATOM_TYPE (cosmolkit.LayeredFingerprintLayers attribute) atom_type (cosmolkit.MmffAngleLookupError property) (cosmolkit.MmffAtomProperties attribute) (cosmolkit.MmffMolPropertiesError property) (cosmolkit.MmffOopLookupError property) (cosmolkit.MmffTorLookupError property) atom_type() (cosmolkit.MmffProperties method) atom_types() (cosmolkit.AtomPairsParameters static method) AtomAddress (class in cosmolkit) AtomAlreadyEmbedded (cosmolkit.Coordinate2DLayoutErrorKind attribute) AtomBetweenModels (cosmolkit.PdbModelTransitionErrorKind attribute) AtomBounds (cosmolkit.ReactionValidationErrorKind attribute) AtomCode (cosmolkit.AtomPairErrorKind attribute) (cosmolkit.OperationErrorKind attribute) (cosmolkit.TopologicalTorsionPathScoreErrorKind attribute) AtomCodeError AtomCodeErrorKind (class in cosmolkit) AtomCodeExplanation (class in cosmolkit) AtomCodeExplanationError AtomCodeExplanationErrorKind (class in cosmolkit) AtomCodeUnderflow (cosmolkit.TopologicalTorsionPathScoreErrorKind attribute) AtomCount (cosmolkit.QueryStateErrorKind attribute) (cosmolkit.XyzReadErrorKind attribute) AtomCountMismatch (cosmolkit.TautomerRunErrorKind attribute) AtomCountTooLarge (cosmolkit.Coordinate2DLayoutErrorKind attribute) AtomFields (cosmolkit.PdbReaderCauseKind attribute) atomic_number (cosmolkit.Atom attribute) (cosmolkit.AtomQueryPredicate attribute) (cosmolkit.BioAtom attribute) (cosmolkit.Element attribute) (cosmolkit.ElementInfo attribute) (cosmolkit.GraphBoundsError property) (cosmolkit.MoleculeAtom attribute) (cosmolkit.QueryAtom attribute) (cosmolkit.QueryAtomConversionError property) (cosmolkit.QueryStateError property) (cosmolkit.RadicalError property) (cosmolkit.SmartsWriteError property) (cosmolkit.ValenceError property) atomic_numbers() (cosmolkit.Molecule method) atomic_weight (cosmolkit.ElementInfo attribute) AtomicNumber (cosmolkit.AtomQueryPredicateKind attribute) (cosmolkit.GraphBoundsErrorKind attribute) AtomicNumberIn (cosmolkit.AtomQueryPredicateKind attribute) AtomicNumberNotIn (cosmolkit.AtomQueryPredicateKind attribute) AtomId (cosmolkit.AtomSiteIdentityField attribute) (cosmolkit.QueryStateErrorKind attribute) AtomIdentityChanged (cosmolkit.AromaticityErrorKind attribute) AtomIdMismatch (cosmolkit.QueryGraphErrorKind attribute) (cosmolkit.TopologyValidationErrorKind attribute) AtomIdOutOfBounds (cosmolkit.UffTypingErrorKind attribute) AtomIndex (cosmolkit.CxQueryLoweringErrorKind attribute) AtomIndexOutOfBounds (cosmolkit.UffTypingErrorKind attribute) AtomIndexOutOfRange (cosmolkit.CipLabelerErrorKind attribute) (cosmolkit.Coordinate2DLayoutErrorKind attribute) (cosmolkit.MmffMolPropertiesErrorKind attribute) (cosmolkit.TopologicalTorsionPathScoreErrorKind attribute) AtomIndexOverflow (cosmolkit.CoordinateValidationErrorKind attribute) AtomInvariantLength (cosmolkit.AtomPairErrorKind attribute) AtomInvariants (cosmolkit.TopologicalTorsionErrorKind attribute) AtomMapInt (cosmolkit.SmartsWriteErrorKind attribute) AtomMapOutOfRange (cosmolkit.CipRankErrorKind attribute) AtomMappingCount (cosmolkit.TautomerRunErrorKind attribute) AtomMaskLength (cosmolkit.CanonicalRankErrorKind attribute) AtomMaskSize (cosmolkit.FullCopyComponentErrorKind attribute) AtomMetadata (class in cosmolkit) AtomName (class in cosmolkit) AtomNameNotAscii (cosmolkit.PdbLinkRecordErrorKind attribute) AtomNameNotRepresentable (cosmolkit.MmcifAtomSiteGroupingErrorKind attribute) (cosmolkit.PdbAtomFieldErrorKind attribute) AtomNotEmbedded (cosmolkit.Coordinate2DLayoutErrorKind attribute) AtomNotFound (cosmolkit.BioStructureErrorKind attribute) AtomOctahedral (cosmolkit.PotentialStereoType attribute) AtomOutOfRange (cosmolkit.AromaticityErrorKind attribute) (cosmolkit.ConjugationErrorKind attribute) (cosmolkit.DoubleBondStereoErrorKind attribute) (cosmolkit.FragmentWriteInputErrorKind attribute) (cosmolkit.NonbondedFragmentMappingErrorKind attribute) (cosmolkit.PathErrorKind attribute) (cosmolkit.PotentialStereoErrorKind attribute) (cosmolkit.SearchMcsErrorKind attribute) (cosmolkit.SelectedSubstanceGroupCopyErrorKind attribute) (cosmolkit.TautomerRunErrorKind attribute) (cosmolkit.TopologyEditErrorKind attribute) (cosmolkit.TransformErrorKind attribute) (cosmolkit.ValenceErrorKind attribute) AtomPair (cosmolkit.MorganErrorKind attribute) AtomPairAtomCodeResult (class in cosmolkit) AtomPairAtomInvariantsGenerator (class in cosmolkit) AtomPairError AtomPairErrorKind (class in cosmolkit) AtomPairFingerprintParams (class in cosmolkit) AtomPairGeneratorParams (class in cosmolkit) AtomPairReadError AtomPairReadErrorKind (class in cosmolkit) AtomPairsParameters (class in cosmolkit) AtomPathOutOfRange (cosmolkit.PathErrorKind attribute) AtomPathSubsetCopyError AtomPathSubsetCopyErrorKind (class in cosmolkit) AtomPositionParams (class in cosmolkit) AtomProperty (cosmolkit.AtomPathSubsetCopyErrorKind attribute) (cosmolkit.CipLabelerErrorKind attribute) (cosmolkit.CxQueryLoweringErrorKind attribute) (cosmolkit.EnumerationErrorKind attribute) (cosmolkit.FragmentWriteInputErrorKind attribute) (cosmolkit.HydrogenErrorKind attribute) (cosmolkit.LegacyStereoErrorKind attribute) (cosmolkit.Mol2ReadErrorKind attribute) (cosmolkit.MolProcessingErrorKind attribute) (cosmolkit.OperationErrorKind attribute) (cosmolkit.ParserCarrierErrorKind attribute) (cosmolkit.PathErrorKind attribute) (cosmolkit.PdbPostprocessErrorKind attribute) (cosmolkit.ReactionProductErrorKind attribute) (cosmolkit.SanitizeErrorKind attribute) (cosmolkit.ScaffoldErrorKind attribute) (cosmolkit.SdfReadErrorKind attribute) (cosmolkit.SmartsParseErrorKind attribute) (cosmolkit.SmilesParseErrorKind attribute) (cosmolkit.StereoErrorKind attribute) (cosmolkit.TautomerRunErrorKind attribute) (cosmolkit.TopologyEditErrorKind attribute) AtomPropertyError AtomPropertyErrorKind (class in cosmolkit) AtomPropertyIndex (cosmolkit.OperationErrorKind attribute) AtomPropertyReadError AtomPropertyReadErrorKind (class in cosmolkit) AtomPropertyWrite (cosmolkit.SmartsWriteErrorKind attribute) AtomQueryPredicate (class in cosmolkit) AtomQueryPredicateKind (class in cosmolkit) AtomRangeBounds (class in cosmolkit) AtomRangeBoundsKind (class in cosmolkit) AtomRangeDataFunction (class in cosmolkit) AtomRangeDataFunctionKind (class in cosmolkit) AtomRangeQuery (class in cosmolkit) AtomRingSize (cosmolkit.AtomRangeDataFunctionKind attribute) atoms (cosmolkit.BioMmcifWriteParams attribute) (cosmolkit.BioResidue attribute) (cosmolkit.BioStructure attribute) (cosmolkit.BioStructureParts attribute) (cosmolkit.CipLabelOptions attribute) (cosmolkit.FragmentCxSmilesWriteParams attribute) (cosmolkit.FragmentSmilesWriteParams attribute) (cosmolkit.MmffMolPropertiesError property) (cosmolkit.MmffProperties attribute) (cosmolkit.Molecule attribute) (cosmolkit.MoleculeBuilder attribute) (cosmolkit.Protein attribute) (cosmolkit.ProteinChainRef attribute) (cosmolkit.ProteinResidueRef attribute) (cosmolkit.ProteinSelectionSummary attribute) (cosmolkit.ScaffoldError property) (cosmolkit.SerialCoordinateCountError property) (cosmolkit.StereoGroup attribute) Atoms (cosmolkit.SubstanceGroupAtomList attribute) atoms (cosmolkit.TautomerMoleculeView attribute) (cosmolkit.TopologyBlock attribute) (cosmolkit.UffBuilderError property) atoms_per_bit (cosmolkit.BatchFingerprintAdditionalOutput attribute) (cosmolkit.FingerprintAdditionalOutput attribute) AtomScalar (cosmolkit.MmcifAtomSiteGroupingErrorKind attribute) AtomSelectionLength (cosmolkit.KekulizeErrorKind attribute) AtomSiteIdentityField (class in cosmolkit) AtomSites (cosmolkit.BioMmcifReadStage attribute) AtomsNotBonded (cosmolkit.TransformErrorKind attribute) AtomSourceIds (class in cosmolkit) AtomSpec (class in cosmolkit) AtomSquarePlanar (cosmolkit.PotentialStereoType attribute) AtomSymbol (cosmolkit.XyzReadErrorKind attribute) AtomSymbolLength (cosmolkit.CanonicalRankErrorKind attribute) AtomSymbolsTooShort (cosmolkit.FragmentWriteInputErrorKind attribute) AtomTetrahedral (cosmolkit.PotentialStereoType attribute) AtomTrigonalBipyramidal (cosmolkit.PotentialStereoType attribute) AtomType (cosmolkit.AtomQueryPredicateKind attribute) AtomTypeAtomicNumber (cosmolkit.SmartsWriteErrorKind attribute) AtomTypePbciMissing (cosmolkit.MmffMolPropertiesErrorKind attribute) AtomTypePropertiesMissing (cosmolkit.MmffMolPropertiesErrorKind attribute) ATP (cosmolkit.ResidueCode attribute) AtropCcw (cosmolkit.BondStereo attribute) AtropCw (cosmolkit.BondStereo attribute) atropisomer (cosmolkit.BondDirectionStereoError property) Atropisomer (cosmolkit.BondDirectionStereoErrorKind attribute) atropisomer (cosmolkit.CipLabelerError property) Atropisomer (cosmolkit.CipLabelerErrorKind attribute) atropisomer (cosmolkit.GenerationError property) Atropisomer (cosmolkit.GenerationErrorKind attribute) atropisomer (cosmolkit.LegacyStereoError property) Atropisomer (cosmolkit.LegacyStereoErrorKind attribute) (cosmolkit.MolProcessingErrorKind attribute) atropisomer (cosmolkit.MolWriteError property) Atropisomer (cosmolkit.MolWriteErrorKind attribute) atropisomer (cosmolkit.StereoError property) Atropisomer (cosmolkit.StereoErrorKind attribute) atropisomer (cosmolkit.WedgeError property) Atropisomer (cosmolkit.WedgeErrorKind attribute) AtropisomerDependencyUnavailable (cosmolkit.PotentialStereoErrorKind attribute) AtropisomerError AtropisomerErrorKind (class in cosmolkit) Atropisomers (cosmolkit.SanitizeErrorKind attribute) AttachmentExpansion (cosmolkit.MolPostErrorKind attribute) (cosmolkit.MolProcessingErrorKind attribute) AttachmentExpansionError AttachmentExpansionErrorKind (class in cosmolkit) AttachmentValue (cosmolkit.MolPostErrorKind attribute) attribute (cosmolkit.XmlParseError property) AttributesLimitReached (cosmolkit.XmlParseErrorKind attribute) AU (cosmolkit.Element attribute) AUGMENTED_ATOM (cosmolkit.AvalonFingerprintFlags attribute) AUGMENTED_BOND (cosmolkit.AvalonFingerprintFlags attribute) auth_all (cosmolkit.BioMmcifWriteParams attribute) auth_chain_id (cosmolkit.ChainSourceIds attribute) author (cosmolkit.BioMmcifWriteParams attribute) author_determined (cosmolkit.BioAssembly attribute) AuthorChainIdNotRepresentable (cosmolkit.MmcifAtomSiteGroupingErrorKind attribute) authors (cosmolkit.BioMetadata attribute) Auto (cosmolkit.CxCoordinateSelection attribute) (cosmolkit.MolCoordinateSelection attribute) auto() (cosmolkit.ReactionCoordinateSelection static method) AutomaticForceFieldConstructionError AutomaticForceFieldConstructionErrorKind (class in cosmolkit) AutomaticObservationUnavailable (cosmolkit.ThreadCountErrorKind attribute) AutoRemapContract (cosmolkit.OperationErrorKind attribute) aux_info (cosmolkit.InchiResult attribute) available (cosmolkit.EmbedFailureCountError property) AvalonConversion (cosmolkit.AvalonEngineErrorKind attribute) AvalonEngineError AvalonEngineErrorKind (class in cosmolkit) AvalonFingerprintError AvalonFingerprintErrorKind (class in cosmolkit) AvalonFingerprintFlags (class in cosmolkit) AvalonFingerprintParams (class in cosmolkit) AxialBondOutOfRange (cosmolkit.AtropisomerErrorKind attribute) axis (cosmolkit.BoundsMatrixError property) (cosmolkit.CoordinateValidationError property) (cosmolkit.TransformError property) AZI (cosmolkit.ResidueCode attribute) B b (cosmolkit.BioCrystalCell attribute) B (cosmolkit.Element attribute) B3E (cosmolkit.ResidueCode attribute) B3P (cosmolkit.ResidueCode attribute) B7G (cosmolkit.ResidueCode attribute) b_iso (cosmolkit.BioAtom attribute) (cosmolkit.BioAtomRow attribute) b_wilson (cosmolkit.BioExperimentInfo attribute) BA (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) bad (cosmolkit.SourceNumericStreamState attribute) BadAtropisomerBondConfig (cosmolkit.CipLabelerErrorKind attribute) BadAtropisomerBondFoci (cosmolkit.CipLabelerErrorKind attribute) BadBondOrder (cosmolkit.ForceFieldKernelErrorKind attribute) BadBondType (cosmolkit.ValenceErrorKind attribute) BadBounds (cosmolkit.ForceFieldKernelErrorKind attribute) BadDoubleBondStereo (cosmolkit.EmbedFailureCause attribute) BadFixedPoint (cosmolkit.ForceFieldKernelErrorKind attribute) BadIndex (cosmolkit.ForceFieldKernelErrorKind attribute) BadInputFile (cosmolkit.TautomerCatalogErrorKind attribute) BadRoot (cosmolkit.JsonErrorKind attribute) BadSp2BondConfig (cosmolkit.CipLabelerErrorKind attribute) BadSp2BondFoci (cosmolkit.CipLabelerErrorKind attribute) BadStreamContents (cosmolkit.TautomerCatalogErrorKind attribute) BadTetrahedralConfig (cosmolkit.CipLabelerErrorKind attribute) basic (cosmolkit.BioRefinementInfo attribute) basin_thresh (cosmolkit.EmbedParams attribute) BatchError BatchErrorMode (class in cosmolkit) batches() (cosmolkit.SdfDataset method) (cosmolkit.SdfReader method) (cosmolkit.SdfRecordStream method) BatchExportParams (class in cosmolkit) BatchExportReport (class in cosmolkit) BatchFingerprintAdditionalOutput (class in cosmolkit) BatchFingerprintOutput (class in cosmolkit) BatchFingerprintOutputError BatchFingerprintOutputErrorKind (class in cosmolkit) BatchImageError BatchImageErrorKind (class in cosmolkit) BatchImageParams (class in cosmolkit) BatchParams (class in cosmolkit) BatchQueryParams (class in cosmolkit) BatchValidationError BCN (cosmolkit.ResidueCode attribute) BE (cosmolkit.Element attribute) BE7 (cosmolkit.ResidueCode attribute) beamline (cosmolkit.BioDiffractionInfo attribute) before (cosmolkit.KekulizeError property) begin (cosmolkit.AdjacencyError property) (cosmolkit.AromaticityError property) (cosmolkit.Bond attribute) (cosmolkit.KekulizeError property) (cosmolkit.McsError property) (cosmolkit.QueryGraphError property) (cosmolkit.RingFindingError property) (cosmolkit.SubstructMatchError property) (cosmolkit.TopologyEditError property) (cosmolkit.TopologyValidationError property) (cosmolkit.ValenceError property) begin_atom (cosmolkit.SmartsParseError property) begin_atom_index (cosmolkit.UffTorsionBondQueryError property) BEGINDASH (cosmolkit.BondDirection attribute) BeginDash (cosmolkit.BondDirection attribute) BEGINWEDGE (cosmolkit.BondDirection attribute) BeginWedge (cosmolkit.BondDirection attribute) BEQ (cosmolkit.ResidueCode attribute) best_alignment_to() (cosmolkit.Molecule method) best_alignment_to_with_params() (cosmolkit.Molecule method) best_rmsd_to() (cosmolkit.Molecule method) best_rmsd_to_with_params() (cosmolkit.Molecule method) BestAlignmentParameters (class in cosmolkit) beta (cosmolkit.BioCrystalCell attribute) BFD (cosmolkit.ResidueCode attribute) BGC (cosmolkit.ResidueCode attribute) BH (cosmolkit.Element attribute) BI (cosmolkit.Element attribute) BIDIRECTIONAL_CONECT (cosmolkit.PdbWriteFlags attribute) bin_count (cosmolkit.BioRefinementInfo attribute) bin_prop_len (cosmolkit.DescriptorError property) bins (cosmolkit.BioRefinementInfo attribute) bins_len (cosmolkit.DescriptorError property) Bio (cosmolkit.MmcifCrystalInfoErrorKind attribute) bio_from_mmcif() (in module cosmolkit) bio_from_pdb() (in module cosmolkit) bio_structure_data (cosmolkit.PdbCrystalError attribute) BioAssembly (class in cosmolkit) BioAssemblyGenerator (class in cosmolkit) BioAssemblyOperator (class in cosmolkit) BioAssemblySpecialKind (class in cosmolkit) BioAsu (class in cosmolkit) BioAtom (class in cosmolkit) BioAtomRow (class in cosmolkit) BioBasicRefinementInfo (class in cosmolkit) BioCalcFlag (class in cosmolkit) BioChain (class in cosmolkit) BioChainRow (class in cosmolkit) BioCisPep (class in cosmolkit) BioConnection (class in cosmolkit) BioConnectionKind (class in cosmolkit) BioCoordinateBlock (class in cosmolkit) BioCoordinateFormat (class in cosmolkit) BioCrystalCell (class in cosmolkit) BioCrystalInfo (class in cosmolkit) BioDiffractionInfo (class in cosmolkit) BioEntityDbRef (class in cosmolkit) BioEntityRow (class in cosmolkit) BioExperimentalCrystalInfo (class in cosmolkit) BioExperimentInfo (class in cosmolkit) BioHelix (class in cosmolkit) BioHelixClass (class in cosmolkit) BioMetadata (class in cosmolkit) BioMmcifReadError BioMmcifReadStage (class in cosmolkit) BioMmcifWriteError BioMmcifWriteErrorKind (class in cosmolkit) BioMmcifWriteParams (class in cosmolkit) BioModel (class in cosmolkit) BioModelRow (class in cosmolkit) BioModRes (class in cosmolkit) BioMolecule (cosmolkit.MolecularIoErrorKind attribute) BioMoleculeConversionError BioMoleculeConversionErrorKind (class in cosmolkit) BioMoleculeError BioMoleculeErrorKind (class in cosmolkit) BioMoleculeParams (class in cosmolkit) BioNcsOperator (class in cosmolkit) BioOperationError BioOperationErrorKind (class in cosmolkit) BioPdbReadError BioPdbReadParams (class in cosmolkit) BioPdbReadStage (class in cosmolkit) BioPdbWriteError BioPdbWriteErrorKind (class in cosmolkit) BioPdbWriteParams (class in cosmolkit) BioReadError BioReadErrorKind (class in cosmolkit) BioReadParams (class in cosmolkit) BioRefinementInfo (class in cosmolkit) BioRefinementRestraint (class in cosmolkit) BioReflectionsInfo (class in cosmolkit) BioResidue (class in cosmolkit) BioResidueRow (class in cosmolkit) BioRowChainError BioRowChainErrorKind (class in cosmolkit) BioRowModelError BioRowModelErrorKind (class in cosmolkit) BioRowSpan (class in cosmolkit) BioRowTraverseError BioRowTraverseErrorKind (class in cosmolkit) BioSelection (class in cosmolkit) BioSelectionCopyCause BioSelectionCopyCauseKind (class in cosmolkit) BioSelectionCopyError BioSelectionMatchError BioSelectionParseError BioSelectionParseErrorKind (class in cosmolkit) BioSheet (class in cosmolkit) BioSiftsUnpResidue (class in cosmolkit) BioSoftwareClassification (class in cosmolkit) BioSoftwareItem (class in cosmolkit) BioStrand (class in cosmolkit) BioStructure (class in cosmolkit) BioStructureData (cosmolkit.PdbCrystalErrorKind attribute) BioStructureError BioStructureErrorKind (class in cosmolkit) BioStructureParts (class in cosmolkit) BioStructureSourceState (class in cosmolkit) BioTlsGroup (class in cosmolkit) BioTlsSelection (class in cosmolkit) BioTransform (class in cosmolkit) bit (cosmolkit.MaccsFingerprintError property) bit_count (cosmolkit.EnumerationError property) bit_flags (cosmolkit.AvalonFingerprintParams attribute) bit_info (cosmolkit.TopologicalFingerprintOutput attribute) (cosmolkit.TopologicalFingerprintOutputRequest attribute) (cosmolkit.TopologicalFingerprintResult attribute) bit_info_map (cosmolkit.BatchFingerprintAdditionalOutput attribute) (cosmolkit.FingerprintAdditionalOutput attribute) bit_paths (cosmolkit.BatchFingerprintAdditionalOutput attribute) (cosmolkit.FingerprintAdditionalOutput attribute) bit_width (cosmolkit.KekulizeError property) BitLengthMismatch (cosmolkit.FingerprintErrorKind attribute) (cosmolkit.PatternFingerprintErrorKind attribute) bits (cosmolkit.AvalonFingerprintFlags attribute) (cosmolkit.CxSmilesFields attribute) (cosmolkit.LayeredFingerprintLayers attribute) (cosmolkit.OperationDerivedState attribute) (cosmolkit.OperationSemanticPreconditions attribute) (cosmolkit.PdbReadFlags attribute) (cosmolkit.PdbWriteFlags attribute) (cosmolkit.SanitizeError property) (cosmolkit.SanitizeOperations attribute) bits_per_entry (cosmolkit.LegacyTopologicalTorsionParams attribute) bits_per_feature (cosmolkit.AtomPairFingerprintParams attribute) (cosmolkit.AtomPairGeneratorParams attribute) (cosmolkit.MorganFingerprintParams attribute) (cosmolkit.MorganGeneratorParams attribute) (cosmolkit.MorganSettings attribute) (cosmolkit.TopologicalTorsionFingerprintParams attribute) (cosmolkit.TopologicalTorsionGeneratorParams attribute) (cosmolkit.TopologicalTorsionSettings attribute) BK (cosmolkit.Element attribute) block (cosmolkit.MmjsonStructureError property) (cosmolkit.OperationError property) block_name (cosmolkit.BioMmcifWriteParams attribute) block_number (cosmolkit.CoordinateBlockSelectionError property) BlockCheckedOut (cosmolkit.OperationErrorKind attribute) BlockKeyPrefix (cosmolkit.MmjsonStructureErrorKind attribute) BlockNotCheckedOut (cosmolkit.OperationErrorKind attribute) BlockNotObject (cosmolkit.MmjsonStructureErrorKind attribute) BMA (cosmolkit.ResidueCode attribute) BME (cosmolkit.ResidueCode attribute) BMT (cosmolkit.ResidueCode attribute) Bndk (cosmolkit.MmffParamTable attribute) BNG (cosmolkit.ResidueCode attribute) BOG (cosmolkit.ResidueCode attribute) Bond (class in cosmolkit) bond (cosmolkit.AdjacencyError property) (cosmolkit.AromaticityError property) (cosmolkit.AtropisomerError property) (cosmolkit.CipLabelerError property) (cosmolkit.CipRankError property) (cosmolkit.ConjugationError property) (cosmolkit.Coordinate2DLayoutError property) (cosmolkit.CxQueryLoweringError property) (cosmolkit.DoubleBondStereoError property) (cosmolkit.EnumerationError property) (cosmolkit.HydrogenError property) (cosmolkit.KekulizeError property) (cosmolkit.MatrixError property) (cosmolkit.McsError property) Bond (cosmolkit.MmffParamTable attribute) bond (cosmolkit.PotentialStereoError property) (cosmolkit.QueryGraphError property) (cosmolkit.QueryMatchContextError property) (cosmolkit.ReactionProductError property) (cosmolkit.RingFindingError property) Bond (cosmolkit.SdfPropertyListTarget attribute) bond (cosmolkit.SdfWriteError property) (cosmolkit.SearchMcsError property) (cosmolkit.SelectedBondCopyError property) (cosmolkit.SelectedSubstanceGroupCopyError property) (cosmolkit.SGroupCState attribute) (cosmolkit.SmartsWriteError property) (cosmolkit.SmilesParseError property) (cosmolkit.StereoError property) (cosmolkit.StereoOrderError property) (cosmolkit.TautomerRunError property) (cosmolkit.TopologyEditError property) (cosmolkit.TopologyValidationError property) (cosmolkit.TransformError property) (cosmolkit.ValenceError property) (cosmolkit.WedgeError property) bond() (cosmolkit.Molecule method) (cosmolkit.TautomerMoleculeView method) BOND_ATROP_CCW (cosmolkit.PotentialStereoDescriptor attribute) BOND_ATROP_CW (cosmolkit.PotentialStereoDescriptor attribute) BOND_ATROPISOMER (cosmolkit.CxSmilesFields attribute) (cosmolkit.PotentialStereoType attribute) bond_between_atoms() (cosmolkit.MoleculeBuilder method) BOND_CFG (cosmolkit.CxSmilesFields attribute) BOND_CIS (cosmolkit.PotentialStereoDescriptor attribute) bond_comparator (cosmolkit.McsParameters attribute) bond_compare_parameters (cosmolkit.McsParameters attribute) bond_copy (cosmolkit.AtomPathSubsetCopyError property) bond_count (cosmolkit.AromaticityError property) (cosmolkit.AtropisomerError property) (cosmolkit.CipLabelerError property) (cosmolkit.ConjugationError property) (cosmolkit.DoubleBondStereoError property) (cosmolkit.FragmentWriteInputError property) (cosmolkit.MatrixError property) (cosmolkit.McsResult attribute) (cosmolkit.ParserStereoOrderError property) (cosmolkit.QueryGraphError property) (cosmolkit.RingFindingError property) (cosmolkit.SelectedSubstanceGroupCopyError property) (cosmolkit.SmartsWriteError property) (cosmolkit.SmilesParseError property) (cosmolkit.StereoOrderError property) (cosmolkit.TautomerRunError property) (cosmolkit.TopologyEditError property) (cosmolkit.TopologyValidationError property) (cosmolkit.UffTypingError property) (cosmolkit.ValenceError property) (cosmolkit.WedgeError property) BOND_CUMULENE_EVEN (cosmolkit.PotentialStereoType attribute) BOND_DOUBLE (cosmolkit.PotentialStereoType attribute) bond_id (cosmolkit.UffTypingError property) bond_index (cosmolkit.FragmentWriteInputError property) (cosmolkit.ParserStereoOrderError property) (cosmolkit.StereoOrderError property) bond_mapping (cosmolkit.MatchResult attribute) bond_match (cosmolkit.SubstructMatchParams attribute) bond_math (cosmolkit.UffBoundsCause attribute) BOND_ORDER (cosmolkit.LayeredFingerprintLayers attribute) bond_order (cosmolkit.SdfWriteError property) (cosmolkit.UffBondMathError property) (cosmolkit.UffBoundsCause attribute) BOND_PATH (cosmolkit.AvalonFingerprintFlags attribute) bond_properties (cosmolkit.SubstructMatchParams attribute) bond_property (cosmolkit.EnumerationError property) (cosmolkit.OperationError property) (cosmolkit.ScaffoldError property) bond_property_string() (cosmolkit.Molecule method) bond_rings (cosmolkit.RingSearchResult attribute) bond_rows (cosmolkit.AromaticityError property) bond_symbols (cosmolkit.FragmentCxSmilesWriteParams attribute) (cosmolkit.FragmentSmilesWriteParams attribute) BOND_TRANS (cosmolkit.PotentialStereoDescriptor attribute) bond_value (cosmolkit.LegacyStereoError property) (cosmolkit.ReactionProductError property) (cosmolkit.TautomerRunError property) BondAtomMismatch (cosmolkit.CxQueryLoweringErrorKind attribute) BondAtomNotEndpoint (cosmolkit.SmartsWriteErrorKind attribute) BondAtomOutOfRange (cosmolkit.AdjacencyErrorKind attribute) BondAtropCcw (cosmolkit.PotentialStereoDescriptor attribute) BondAtropCw (cosmolkit.PotentialStereoDescriptor attribute) BondAtropisomer (cosmolkit.PotentialStereoType attribute) BondCis (cosmolkit.PotentialStereoDescriptor attribute) BondCopy (cosmolkit.AtomPathSubsetCopyErrorKind attribute) BondCount (cosmolkit.QueryStateErrorKind attribute) BondCountMismatch (cosmolkit.TautomerRunErrorKind attribute) BondCumuleneEven (cosmolkit.PotentialStereoType attribute) BondDirection (class in cosmolkit) BondDirectionStereo (cosmolkit.MolProcessingErrorKind attribute) BondDirectionStereoError BondDirectionStereoErrorKind (class in cosmolkit) BondDouble (cosmolkit.PotentialStereoType attribute) BondEndpointOutOfRange (cosmolkit.TopologyValidationErrorKind attribute) BondEndpoints (cosmolkit.QueryStateErrorKind attribute) BondEndPointsParse (cosmolkit.TopologyEditErrorKind attribute) BondEndPointsParseErrorKind (class in cosmolkit) BondId (cosmolkit.QueryStateErrorKind attribute) BondIdentityChanged (cosmolkit.AromaticityErrorKind attribute) BondIdMismatch (cosmolkit.QueryGraphErrorKind attribute) (cosmolkit.TopologyValidationErrorKind attribute) BondIdOutOfBounds (cosmolkit.UffTypingErrorKind attribute) BondIndex (cosmolkit.CxQueryLoweringErrorKind attribute) BondIndexOutOfRange (cosmolkit.CipLabelerErrorKind attribute) (cosmolkit.ForceFieldKernelErrorKind attribute) (cosmolkit.ParserStereoOrderErrorKind attribute) BondIndexSourceWidth (cosmolkit.StereoOrderErrorKind attribute) BondMappingCount (cosmolkit.TautomerRunErrorKind attribute) BondMaskLength (cosmolkit.CanonicalRankErrorKind attribute) BondMath (cosmolkit.UffBoundsCauseKind attribute) (cosmolkit.UffTypingErrorKind attribute) BondNotIncident (cosmolkit.CipLabelerErrorKind attribute) (cosmolkit.StereoOrderErrorKind attribute) BondOrder (class in cosmolkit) (cosmolkit.SdfWriteErrorKind attribute) (cosmolkit.UffBoundsCauseKind attribute) BondOutOfRange (cosmolkit.AromaticityErrorKind attribute) (cosmolkit.ConjugationErrorKind attribute) (cosmolkit.DoubleBondStereoErrorKind attribute) (cosmolkit.FragmentWriteInputErrorKind attribute) (cosmolkit.SearchMcsErrorKind attribute) (cosmolkit.SelectedSubstanceGroupCopyErrorKind attribute) (cosmolkit.StereoOrderErrorKind attribute) (cosmolkit.TautomerRunErrorKind attribute) (cosmolkit.TopologyEditErrorKind attribute) (cosmolkit.WedgeErrorKind attribute) BondProperty (cosmolkit.AtomPathSubsetCopyErrorKind attribute) (cosmolkit.CxQueryLoweringErrorKind attribute) (cosmolkit.EnumerationErrorKind attribute) (cosmolkit.HydrogenErrorKind attribute) (cosmolkit.OperationErrorKind attribute) (cosmolkit.PathErrorKind attribute) (cosmolkit.SanitizeErrorKind attribute) (cosmolkit.ScaffoldErrorKind attribute) (cosmolkit.SmartsParseErrorKind attribute) (cosmolkit.SmilesParseErrorKind attribute) BondQueryPredicate (class in cosmolkit) BondQueryPredicateKind (class in cosmolkit) bonds (cosmolkit.CipLabelOptions attribute) (cosmolkit.FragmentCxSmilesWriteParams attribute) (cosmolkit.FragmentSmilesWriteParams attribute) (cosmolkit.Molecule attribute) (cosmolkit.MoleculeBuilder attribute) (cosmolkit.StereoGroup attribute) (cosmolkit.TautomerMoleculeView attribute) (cosmolkit.TopologyBlock attribute) BondSelectionLength (cosmolkit.KekulizeErrorKind attribute) BondSpec (class in cosmolkit) BondStereo (class in cosmolkit) BondSymbolLength (cosmolkit.CanonicalRankErrorKind attribute) BondSymbolsTooShort (cosmolkit.FragmentWriteInputErrorKind attribute) BondTrans (cosmolkit.PotentialStereoDescriptor attribute) BondUpdate (cosmolkit.AtropisomerErrorKind attribute) BondValue (cosmolkit.CipLabelerErrorKind attribute) (cosmolkit.DoubleBondStereoErrorKind attribute) (cosmolkit.LegacyStereoErrorKind attribute) (cosmolkit.MolProcessingErrorKind attribute) (cosmolkit.PotentialStereoErrorKind attribute) (cosmolkit.ReactionProductErrorKind attribute) (cosmolkit.SdfReadErrorKind attribute) (cosmolkit.TautomerRunErrorKind attribute) BondValueError BondValueErrorKind (class in cosmolkit) Bool (cosmolkit.PropertyValueKind attribute) Bool() (cosmolkit.PropertyValue static method) BothAngleBondsInRing (cosmolkit.TransformErrorKind attribute) bound (cosmolkit.ForceFieldKernelError property) BoundKind (class in cosmolkit) bounds (cosmolkit.AtomRangeQuery attribute) (cosmolkit.BoundsQueryError property) Bounds (cosmolkit.BoundsQueryErrorKind attribute) bounds (cosmolkit.GenerationError property) Bounds (cosmolkit.GenerationErrorKind attribute) (cosmolkit.GraphBoundsErrorKind attribute) bounds_mat_force_scaling (cosmolkit.EmbedParams attribute) BoundsMatrixError BoundsMatrixErrorKind (class in cosmolkit) BoundsQueryError BoundsQueryErrorKind (class in cosmolkit) box_size_mult (cosmolkit.EmbedParams attribute) BR (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) brackets (cosmolkit.SGroupDisplay attribute) branch (cosmolkit.CanonicalRankError property) (cosmolkit.SubstructMatchError property) branch_count (cosmolkit.AtomCodeExplanation attribute) Branched (cosmolkit.EntityKind attribute) branched_paths (cosmolkit.LayeredFingerprintParams attribute) (cosmolkit.TopologicalFingerprintParams attribute) BRO (cosmolkit.ResidueCode attribute) BrokenPipe (cosmolkit.IoErrorKind attribute) BRU (cosmolkit.ResidueCode attribute) BTB (cosmolkit.ResidueCode attribute) BU1 (cosmolkit.ResidueCode attribute) BU2 (cosmolkit.ResidueCode attribute) BU3 (cosmolkit.ResidueCode attribute) BUF (cosmolkit.ResidueInfoKind attribute) Buffer (cosmolkit.ResidueKind attribute) buffer_len (cosmolkit.ForceFieldKernelError property) build (cosmolkit.MoleculeFragmentsFailure property) Build (cosmolkit.MoleculeFragmentsFailureKind attribute) build() (cosmolkit.MoleculeBuilder method) Builder (cosmolkit.ForceFieldConstructionErrorKind attribute) builder (cosmolkit.MmffOptimizationFailure property) Builder (cosmolkit.MmffOptimizationFailureKind attribute) buried_surface_area (cosmolkit.BioAssembly attribute) byte (cosmolkit.PdbCisPepRecordError attribute) (cosmolkit.PdbLinkRecordError attribute) (cosmolkit.PdbResidueKeyError property) (cosmolkit.PdbSsbondRecordError attribute) (cosmolkit.UIntLexicalReadError property) byte_count (cosmolkit.UffBuilderError property) byte_index (cosmolkit.UffBuilderError property) byte_len (cosmolkit.SdfRecordMetadata attribute) byte_offset (cosmolkit.JsonError property) (cosmolkit.SdfReadError property) (cosmolkit.SdfRecordMetadata attribute) byte_range (cosmolkit.SdfRecordMetadata attribute) bytes (cosmolkit.PdbAtomFieldError attribute) bytes_consumed (cosmolkit.SdfRecordStream attribute) C c (cosmolkit.BioCrystalCell attribute) C (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) C10 (cosmolkit.ResidueCode attribute) C15 (cosmolkit.ResidueCode attribute) C8E (cosmolkit.ResidueCode attribute) CA (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) CAC (cosmolkit.ResidueCode attribute) Cache (cosmolkit.UffParameterQueryErrorKind attribute) CachePoisoned (cosmolkit.DescriptorReadErrorKind attribute) CAF (cosmolkit.ResidueCode attribute) calc_flag (cosmolkit.BioAtomRow attribute) Calculated (cosmolkit.BioCalcFlag attribute) calculated (cosmolkit.ValenceError property) calculation_flag (cosmolkit.BioAtom attribute) Callback (cosmolkit.McsProgressErrorKind attribute) callback (cosmolkit.TautomerParams attribute) (cosmolkit.TautomerRunError property) Callback (cosmolkit.TautomerRunErrorKind attribute) Canceled (cosmolkit.TautomerEnumerationStatus attribute) CandidateAtomOutOfRange (cosmolkit.KekulizeErrorKind attribute) CandidateTraversalDuplicate (cosmolkit.AtropisomerErrorKind attribute) CandidateTraversalMissing (cosmolkit.AtropisomerErrorKind attribute) CandidateTraversalOutOfRange (cosmolkit.AtropisomerErrorKind attribute) CandidateTraversalUnexpected (cosmolkit.AtropisomerErrorKind attribute) CannotNormalizeZeroLengthVector (cosmolkit.ConformerErrorKind attribute) CannotParseSmarts (cosmolkit.TautomerTransformErrorKind attribute) canonical (cosmolkit.KekulizeParams attribute) (cosmolkit.ReactionWriteParams attribute) (cosmolkit.SmilesWriteParams attribute) canonical_one_letter_code (cosmolkit.ResidueInfo attribute) canonical_orientation (cosmolkit.Coordinate2DParams attribute) canonical_rank (cosmolkit.CleanupError property) (cosmolkit.KekulizeError property) (cosmolkit.SmilesParseError property) canonical_smiles (cosmolkit.TautomerEnumeration attribute) canonical_tautomer() (cosmolkit.Molecule method) (cosmolkit.TautomerEnumeration method) canonical_tautomer_from_molecules() (in module cosmolkit) canonical_tautomer_from_molecules_with_params() (in module cosmolkit) canonical_tautomer_with_params() (cosmolkit.Molecule method) (cosmolkit.TautomerEnumeration method) CanonicalRank (cosmolkit.CleanupErrorKind attribute) (cosmolkit.KekulizeErrorKind attribute) (cosmolkit.SmilesParseErrorKind attribute) CanonicalRankError CanonicalRankErrorKind (class in cosmolkit) CanonicalTraversal (cosmolkit.SmartsWriteErrorKind attribute) capability (cosmolkit.MolPostError property) (cosmolkit.MolWriteError property) (cosmolkit.SdfReadError property) carrier (cosmolkit.CanonicalRankError property) (cosmolkit.PathError property) (cosmolkit.SmartsParseError property) (cosmolkit.TopologyEditError property) carrier_identity (cosmolkit.ReactionProductError property) CarrierCount (cosmolkit.AtropisomerErrorKind attribute) CarrierIdentity (cosmolkit.ReactionProductErrorKind attribute) CarrierMismatch (cosmolkit.CipLabelerErrorKind attribute) CAS (cosmolkit.ResidueCode attribute) category (cosmolkit.FeatureSpec attribute) (cosmolkit.MmjsonStructureError property) cause (cosmolkit.ConformerOptimizerError property) (cosmolkit.MmffParamParseError property) (cosmolkit.OperationError property) (cosmolkit.ProteinProjectionError property) (cosmolkit.UffBoundsError property) CBM (cosmolkit.ResidueCode attribute) CBR (cosmolkit.ResidueCode attribute) CBX (cosmolkit.ResidueCode attribute) cc_fo_fc_free (cosmolkit.BioBasicRefinementInfo attribute) cc_fo_fc_work (cosmolkit.BioBasicRefinementInfo attribute) cc_intensity_free (cosmolkit.BioBasicRefinementInfo attribute) cc_intensity_work (cosmolkit.BioBasicRefinementInfo attribute) CCC (cosmolkit.ResidueCode attribute) ccd (cosmolkit.PdbStructureFinalizationError attribute) Ccd (cosmolkit.PdbStructureFinalizationErrorKind attribute) CcdRestoration (cosmolkit.BioMmcifReadStage attribute) CCN (cosmolkit.ResidueCode attribute) CD (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) CE (cosmolkit.Element attribute) CE1 (cosmolkit.ResidueCode attribute) cell (cosmolkit.BioCrystalInfo attribute) (cosmolkit.BioMmcifWriteParams attribute) (cosmolkit.DescriptorError property) (cosmolkit.MmffParamParseCause attribute) center (cosmolkit.StereoError property) (cosmolkit.StereoOrderError property) (cosmolkit.TetrahedralStereo attribute) (cosmolkit.WedgeError property) center_atom_index (cosmolkit.UffBuilderError property) CenterBondMissingAfterSourceSuccess (cosmolkit.UffTypingErrorKind attribute) centered_on (cosmolkit.PotentialStereoInfo attribute) CenterNotIncident (cosmolkit.WedgeErrorKind attribute) CenterOutOfRange (cosmolkit.StereoOrderErrorKind attribute) CentralParameterSlotMissingAfterSourceSuccess (cosmolkit.UffTypingErrorKind attribute) centre (cosmolkit.Coordinate2DLayoutError property) CF (cosmolkit.Element attribute) CGU (cosmolkit.ResidueCode attribute) chain (cosmolkit.BioPdbWriteError property) Chain (cosmolkit.BioRowTraverseErrorKind attribute) chain (cosmolkit.BioTlsSelection attribute) (cosmolkit.MmcifTlsInfoError property) (cosmolkit.PdbModelTransitionError property) (cosmolkit.ProteinResidueRef attribute) chain() (cosmolkit.BioStructure method) (cosmolkit.Protein method) chain_id (cosmolkit.BioResidue attribute) (cosmolkit.BioResidueRow attribute) chain_name (cosmolkit.AtomAddress attribute) (cosmolkit.BioModRes attribute) chain_span (cosmolkit.BioModel attribute) (cosmolkit.BioModelRow attribute) ChainKind (class in cosmolkit) ChainNameNotAscii (cosmolkit.PdbCisPepRecordErrorKind attribute) (cosmolkit.PdbLinkRecordErrorKind attribute) (cosmolkit.PdbSsbondRecordErrorKind attribute) ChainNameNotRepresentable (cosmolkit.MmcifCisPepErrorKind attribute) (cosmolkit.MmcifConnectionErrorKind attribute) (cosmolkit.MmcifHelixErrorKind attribute) (cosmolkit.MmcifLabelAddressErrorKind attribute) (cosmolkit.MmcifModResErrorKind attribute) (cosmolkit.MmcifSheetErrorKind attribute) (cosmolkit.PdbAtomFieldErrorKind attribute) (cosmolkit.PdbHelixErrorKind attribute) (cosmolkit.PdbModResErrorKind attribute) (cosmolkit.PdbSheetErrorKind attribute) ChainNameTooLong (cosmolkit.BioPdbWriteErrorKind attribute) chains (cosmolkit.BioAssemblyGenerator attribute) (cosmolkit.BioModel attribute) (cosmolkit.BioStructure attribute) (cosmolkit.BioStructureParts attribute) (cosmolkit.Protein attribute) (cosmolkit.ProteinSelectionSummary attribute) ChainSourceIds (class in cosmolkit) changed (cosmolkit.ReactionApplyResult attribute) character (cosmolkit.SmartsParseError property) Character (cosmolkit.UIntLexicalReadErrorKind attribute) character (cosmolkit.XmlParseError property) charge (cosmolkit.PdbAtomFieldError attribute) Charge (cosmolkit.PdbAtomFieldErrorKind attribute) charge (cosmolkit.TautomerRunError property) ChargeMagnitudeOverflow (cosmolkit.SmartsWriteErrorKind attribute) ChargeOutsideSourceDefinedRange (cosmolkit.ChemCompAtomErrorKind attribute) ChargeSymbolNotRecognised (cosmolkit.TautomerTransformErrorKind attribute) check_non_ascii (cosmolkit.BioPdbReadParams attribute) CheckChiralCenters (cosmolkit.EmbedFailureCause attribute) CheckChiralCenters2 (cosmolkit.EmbedFailureCause attribute) CheckTetrahedralCenters (cosmolkit.EmbedFailureCause attribute) chem_comp (cosmolkit.BioMmcifWriteParams attribute) ChemComp (cosmolkit.BioCoordinateFormat attribute) (cosmolkit.BioReadErrorKind attribute) ChemCompAtomError ChemCompAtomErrorKind (class in cosmolkit) ChemCompModelError ChemCompModelErrorKind (class in cosmolkit) Chemistry (cosmolkit.BioMoleculeConversionErrorKind attribute) ChemistryProblem (class in cosmolkit) ChemistryProblemError ChemistryProblemErrorKind (class in cosmolkit) ChemistryProblemReport (class in cosmolkit) Chg (cosmolkit.MmffParamTable attribute) chi_0() (cosmolkit.Molecule method) chi_0_n() (cosmolkit.Molecule method) chi_0_n_with_params() (cosmolkit.Molecule method) chi_0_v() (cosmolkit.Molecule method) chi_0_v_with_params() (cosmolkit.Molecule method) chi_1() (cosmolkit.Molecule method) chi_1_n() (cosmolkit.Molecule method) chi_1_n_with_params() (cosmolkit.Molecule method) chi_1_v() (cosmolkit.Molecule method) chi_1_v_with_params() (cosmolkit.Molecule method) chi_2_n() (cosmolkit.Molecule method) chi_2_n_with_params() (cosmolkit.Molecule method) chi_2_v() (cosmolkit.Molecule method) chi_2_v_with_params() (cosmolkit.Molecule method) chi_3_n() (cosmolkit.Molecule method) chi_3_n_with_params() (cosmolkit.Molecule method) chi_3_v() (cosmolkit.Molecule method) chi_3_v_with_params() (cosmolkit.Molecule method) chi_4_n() (cosmolkit.Molecule method) chi_4_n_with_params() (cosmolkit.Molecule method) chi_4_v() (cosmolkit.Molecule method) chi_4_v_with_params() (cosmolkit.Molecule method) CHI_ALLENE (cosmolkit.ChiralTag attribute) chi_n_n() (cosmolkit.Molecule method) chi_n_n_with_params() (cosmolkit.Molecule method) chi_n_v() (cosmolkit.Molecule method) chi_n_v_with_params() (cosmolkit.Molecule method) CHI_OCTAHEDRAL (cosmolkit.ChiralTag attribute) CHI_OTHER (cosmolkit.ChiralTag attribute) CHI_SQUAREPLANAR (cosmolkit.ChiralTag attribute) CHI_TETRAHEDRAL (cosmolkit.ChiralTag attribute) CHI_TETRAHEDRAL_CCW (cosmolkit.ChiralTag attribute) CHI_TETRAHEDRAL_CW (cosmolkit.ChiralTag attribute) CHI_TRIGONALBIPYRAMIDAL (cosmolkit.ChiralTag attribute) CHI_UNSPECIFIED (cosmolkit.ChiralTag attribute) chiral_tag (cosmolkit.Atom attribute) (cosmolkit.MoleculeAtom attribute) chiral_tag_code (cosmolkit.Atom attribute) (cosmolkit.MoleculeAtom attribute) chiral_tag_name (cosmolkit.Atom attribute) (cosmolkit.MoleculeAtom attribute) chirality (cosmolkit.AtomCodeExplanation attribute) Chirality (cosmolkit.SanitizeErrorKind attribute) ChiralPermutationMatch (cosmolkit.AtomQueryPredicateKind attribute) ChiralPermutationRead (cosmolkit.StereoOrderErrorKind attribute) ChiralPermutationWrite (cosmolkit.StereoOrderErrorKind attribute) ChiralTag (class in cosmolkit) ChiralTagMatch (cosmolkit.AtomQueryPredicateKind attribute) cid (cosmolkit.BioSelectionParseError property) Cif (cosmolkit.BioMmcifWriteErrorKind attribute) (cosmolkit.BioReadErrorKind attribute) (cosmolkit.MmcifAssemblyErrorKind attribute) (cosmolkit.MmcifCisPepErrorKind attribute) (cosmolkit.MmcifConnectionErrorKind attribute) (cosmolkit.MmcifCrystalInfoErrorKind attribute) (cosmolkit.MmcifEntityInfoErrorKind attribute) (cosmolkit.MmcifHelixErrorKind attribute) (cosmolkit.MmcifModResErrorKind attribute) (cosmolkit.MmcifSheetErrorKind attribute) (cosmolkit.MmcifSiftsUnpErrorKind attribute) (cosmolkit.MmcifTlsInfoErrorKind attribute) (cosmolkit.PdbInputFormatErrorKind attribute) CifCharacter (cosmolkit.MmcifAtomSiteScalarErrorKind attribute) CifDocument (cosmolkit.BioMmcifReadStage attribute) CifInteger (cosmolkit.MmcifAtomSiteScalarErrorKind attribute) CifNumber (cosmolkit.MmcifAtomSiteScalarErrorKind attribute) CifReadError CifReadErrorKind (class in cosmolkit) Cip (cosmolkit.AtomCodeErrorKind attribute) cip_computed (cosmolkit.Molecule attribute) cip_descriptor (cosmolkit.Atom attribute) (cosmolkit.Bond attribute) (cosmolkit.MoleculeAtom attribute) cip_labeler (cosmolkit.OperationError property) cip_neighbor_order (cosmolkit.Atom attribute) (cosmolkit.Bond attribute) (cosmolkit.MoleculeAtom attribute) cip_rank (cosmolkit.Atom attribute) (cosmolkit.LegacyStereoError property) (cosmolkit.MoleculeAtom attribute) CipDescriptor (class in cosmolkit) CipDescriptorError CipDescriptorErrorKind (class in cosmolkit) CipLabelEncoding (cosmolkit.StereoReadErrorKind attribute) CipLabeler (cosmolkit.OperationErrorKind attribute) (cosmolkit.StereoReadErrorKind attribute) CipLabelerError CipLabelerErrorKind (class in cosmolkit) CipLabelOptions (class in cosmolkit) CipProperty (cosmolkit.FragmentWriteInputErrorKind attribute) CipRank (cosmolkit.LegacyStereoErrorKind attribute) CipRankError CipRankErrorKind (class in cosmolkit) CipRanks (cosmolkit.MoleculeHashErrorKind attribute) CipStateContract (cosmolkit.OperationErrorKind attribute) CIR (cosmolkit.ResidueCode attribute) cis (cosmolkit.BioMmcifWriteParams attribute) Cis (cosmolkit.BondStereo attribute) cis_pep_record (cosmolkit.PdbConnectionFinalizationError attribute) CisPepRecord (cosmolkit.PdbConnectionFinalizationErrorKind attribute) cispeps (cosmolkit.BioStructure attribute) (cosmolkit.BioStructureParts attribute) CisPeptides (cosmolkit.BioMmcifReadStage attribute) CisTransBondInvalid (cosmolkit.Coordinate2DLayoutErrorKind attribute) CIT (cosmolkit.ResidueCode attribute) CL (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) Clash (cosmolkit.EmbedFailureCause attribute) CLASS_SPIDERS (cosmolkit.AvalonFingerprintFlags attribute) classification (cosmolkit.BioSoftwareItem attribute) classify (cosmolkit.SerdeJsonError property) clean (cosmolkit.PotentialStereoParams attribute) clean_stereo (cosmolkit.SmilesWriteParams attribute) cleaned_molecule (cosmolkit.PotentialStereoResult attribute) Cleanup (cosmolkit.SanitizeErrorKind attribute) CLEANUP (cosmolkit.SanitizeOperations attribute) Cleanup (cosmolkit.SanitizeStage attribute) CLEANUP_ATROPISOMERS (cosmolkit.SanitizeOperations attribute) CLEANUP_CHIRALITY (cosmolkit.SanitizeOperations attribute) CLEANUP_ORGANOMETALLICS (cosmolkit.SanitizeOperations attribute) cleanup_substructures (cosmolkit.Mol2ReadParams attribute) CleanupAtropisomers (cosmolkit.SanitizeStage attribute) CleanupChirality (cosmolkit.SanitizeStage attribute) CleanupError CleanupErrorKind (class in cosmolkit) CleanupOrganometallics (cosmolkit.SanitizeStage attribute) clear_3d_conformers_() (cosmolkit.Molecule method) clear_conformers (cosmolkit.EmbedParams attribute) clear_existing_2d (cosmolkit.Coordinate2DParams attribute) CLO (cosmolkit.ResidueCode attribute) CM (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) CM5 (cosmolkit.ResidueCode attribute) CME (cosmolkit.ResidueCode attribute) CN (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) CO (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) code (cosmolkit.AtomCodeError property) (cosmolkit.AtomCodeExplanationError property) (cosmolkit.AtomPairAtomCodeResult attribute) (cosmolkit.ProteinResidueRef attribute) (cosmolkit.ResidueIdentity attribute) (cosmolkit.ResidueInfo attribute) (cosmolkit.TopologicalTorsionPathScoreError property) code_size() (cosmolkit.AtomPairsParameters static method) Codec (cosmolkit.MoleculeTransferErrorKind attribute) CoincidentCoordinates (cosmolkit.TransformErrorKind attribute) CoincidentPoints (cosmolkit.Coordinate2DLayoutErrorKind attribute) col (cosmolkit.XmlTextPos attribute) collection_date (cosmolkit.BioDiffractionInfo attribute) CollisionBondInvalid (cosmolkit.Coordinate2DLayoutErrorKind attribute) column (cosmolkit.BoundsMatrixError property) (cosmolkit.ChemCompAtomError property) (cosmolkit.CifReadError property) (cosmolkit.CoordinateInputError property) (cosmolkit.JsonError property) Column (cosmolkit.MatrixAxis attribute) column (cosmolkit.McsError property) (cosmolkit.MmffParamParseError property) (cosmolkit.MmjsonStructureError property) (cosmolkit.SerdeJsonError property) (cosmolkit.TransformError property) column_count (cosmolkit.UffParamError property) column_name (cosmolkit.UffParamError property) columns (cosmolkit.CoordinateInputError property) CombinationLevel (cosmolkit.ReactionRunErrorKind attribute) CombinationSize (cosmolkit.ReactionRunErrorKind attribute) compact (cosmolkit.BioMmcifWriteParams attribute) CompId (cosmolkit.AtomSiteIdentityField attribute) Compile (cosmolkit.DescriptorSearchCauseKind attribute) (cosmolkit.UffDefaultTorsionQueryErrorKind attribute) (cosmolkit.UffTorsionBondQueryErrorKind attribute) compile_query() (in module cosmolkit) CompiledQuery (class in cosmolkit) complete_rings_only (cosmolkit.McsAtomCompareParameters attribute) (cosmolkit.McsBondCompareParameters attribute) Completed (cosmolkit.EmbedTermination attribute) completed (cosmolkit.McsResult attribute) Completed (cosmolkit.TautomerEnumerationStatus attribute) CompleteIcosahedral (cosmolkit.BioAssemblySpecialKind attribute) completeness (cosmolkit.BioBasicRefinementInfo attribute) (cosmolkit.BioReflectionsInfo attribute) CompletePoint (cosmolkit.BioAssemblySpecialKind attribute) component (cosmolkit.FingerprintJsonError property) (cosmolkit.ForceFieldError property) (cosmolkit.MmffForceFieldError property) component_index (cosmolkit.MoleculeFragmentsError property) (cosmolkit.MoleculeFragmentsFailure property) (cosmolkit.NonbondedFragmentMappingError property) (cosmolkit.OrderedFragmentBuildError property) component_labels (cosmolkit.OrderedFragmentBuildError property) ComponentAtomOutOfRange (cosmolkit.CanonicalRankErrorKind attribute) ComponentBounds (cosmolkit.ReactionParseErrorKind attribute) ComponentEncoding (cosmolkit.ReactionParseErrorKind attribute) ComponentLabels (cosmolkit.OrderedFragmentBuildErrorKind attribute) components (cosmolkit.MmffBuilderError property) Components (cosmolkit.MmffBuilderErrorKind attribute) CompositeChildCount (cosmolkit.SmartsWriteErrorKind attribute) computed_list_kind (cosmolkit.AtomPropertyError property) (cosmolkit.BondValueError property) (cosmolkit.MoleculePropertyError property) computed_prop_names (cosmolkit.MoleculeProperties attribute) computed_properties (cosmolkit.AtomPathSubsetCopyError property) ComputedListKind (cosmolkit.AtomPropertyErrorKind attribute) (cosmolkit.BondValueErrorKind attribute) (cosmolkit.MoleculePropertyErrorKind attribute) ComputedProperties (cosmolkit.AtomPathSubsetCopyErrorKind attribute) conect (cosmolkit.PdbReaderCause property) Conect (cosmolkit.PdbReaderCauseKind attribute) conect_map (cosmolkit.BioStructureSourceState attribute) conf_id (cosmolkit.EmbedMoleculeResult attribute) (cosmolkit.MmffBuilderError property) conf_ids (cosmolkit.EmbedMultipleConfsResult attribute) ConflictingChiralPermutation (cosmolkit.StereoOrderErrorKind attribute) ConflictingCoordinateSelection (cosmolkit.PdbWriteErrorKind attribute) conformer (cosmolkit.AtropisomerError property) (cosmolkit.CoordinateValidationError property) (cosmolkit.HydrogenError property) (cosmolkit.OperationError property) Conformer (cosmolkit.OperationErrorKind attribute) conformer (cosmolkit.StereoError property) Conformer2D (class in cosmolkit) Conformer3D (class in cosmolkit) conformer_id (cosmolkit.AtomPairFingerprintParams attribute) (cosmolkit.AtomPositionParams attribute) (cosmolkit.Coordinate3DReadError property) (cosmolkit.CoordinateInputError property) (cosmolkit.DistanceMatrix3dParams attribute) (cosmolkit.FullCopyComponentError property) (cosmolkit.MatrixError property) (cosmolkit.MmffEvaluationParams attribute) (cosmolkit.MmffForceFieldParams attribute) (cosmolkit.MmffOptimizationParams attribute) (cosmolkit.Replace3DCoordinatesParams attribute) (cosmolkit.SerialConformerOptimizationError property) (cosmolkit.SerialCoordinateCountError property) (cosmolkit.StructureTagParams attribute) (cosmolkit.TransformError property) (cosmolkit.UffBuilderError property) (cosmolkit.UffConformerResult attribute) (cosmolkit.UffEvaluationParams attribute) (cosmolkit.UffForceFieldParams attribute) (cosmolkit.UffOptimizationParams attribute) (cosmolkit.XyzWriteParams attribute) conformer_ids (cosmolkit.ConformerAlignmentParameters attribute) conformer_results (cosmolkit.MmffOptimizeMoleculeConfsResult attribute) (cosmolkit.UffConformerOptimizationResult attribute) ConformerAlignmentParameters (class in cosmolkit) ConformerAlignmentReport (class in cosmolkit) ConformerAtomCountMismatch (cosmolkit.StereoErrorKind attribute) ConformerError ConformerErrorKind (class in cosmolkit) ConformerIdOverflow (cosmolkit.Coordinate2DErrorKind attribute) (cosmolkit.CoordinateInputErrorKind attribute) (cosmolkit.CoordinateValidationErrorKind attribute) ConformerNotFound (cosmolkit.AlignmentErrorKind attribute) (cosmolkit.Coordinate3DReadErrorKind attribute) (cosmolkit.CoordinateInputErrorKind attribute) (cosmolkit.MatrixErrorKind attribute) (cosmolkit.PdbWriteErrorKind attribute) (cosmolkit.StereoErrorKind attribute) (cosmolkit.TransformErrorKind attribute) (cosmolkit.XyzWriteErrorKind attribute) ConformerNotThreeDimensional (cosmolkit.AtropisomerErrorKind attribute) ConformerOptimization (cosmolkit.UffOptimizationErrorKind attribute) ConformerOptimizerCause (class in cosmolkit) ConformerOptimizerCauseKind (class in cosmolkit) ConformerOptimizerError ConformerRmsd (class in cosmolkit) ConformerRunError conformers (cosmolkit.SerialResultCapacityError property) conformers_2d (cosmolkit.CoordinateBlock attribute) conformers_3d (cosmolkit.CoordinateBlock attribute) (cosmolkit.Molecule attribute) ConformerStage (cosmolkit.UffPreparedOptimizationErrorKind attribute) ConjugatedBondAssignmentLength (cosmolkit.HybridizationErrorKind attribute) ConjugatedBondPresence (cosmolkit.UffTypingInput attribute) Conjugation (cosmolkit.AtropisomerErrorKind attribute) conjugation (cosmolkit.BoundsQueryError property) Conjugation (cosmolkit.BoundsQueryErrorKind attribute) conjugation (cosmolkit.GenerationError property) Conjugation (cosmolkit.GenerationErrorKind attribute) (cosmolkit.SanitizeErrorKind attribute) ConjugationError ConjugationErrorKind (class in cosmolkit) conn (cosmolkit.BioMmcifWriteParams attribute) ConnectedComponents (cosmolkit.Coordinate2DTemplateErrorKind attribute) connection (cosmolkit.PdbStructureFinalizationError attribute) Connection (cosmolkit.PdbStructureFinalizationErrorKind attribute) ConnectionAborted (cosmolkit.IoErrorKind attribute) ConnectionRefused (cosmolkit.IoErrorKind attribute) ConnectionReset (cosmolkit.IoErrorKind attribute) Connections (cosmolkit.BioMmcifReadStage attribute) connections (cosmolkit.BioStructure attribute) (cosmolkit.BioStructureParts attribute) Connectivity (cosmolkit.MorganInvariants attribute) (cosmolkit.ReactionWriteErrorKind attribute) connectivity() (cosmolkit.MorganAtomInvariantsGenerator static method) constant_name (cosmolkit.CrystalffTorsionPreferencesError property) Construction (cosmolkit.AutomaticForceFieldConstructionErrorKind attribute) (cosmolkit.BioMoleculeErrorKind attribute) construction (cosmolkit.ConformerOptimizerCause attribute) Construction (cosmolkit.ConformerOptimizerCauseKind attribute) (cosmolkit.DispatchedUffOptimizationErrorKind attribute) (cosmolkit.MolecularForceFieldErrorKind attribute) (cosmolkit.MolecularIoErrorKind attribute) (cosmolkit.SdfErrorKind attribute) (cosmolkit.SerialUffOptimizationErrorKind attribute) (cosmolkit.SingleConformerOptimizationErrorKind attribute) (cosmolkit.SmilesErrorKind attribute) construction (cosmolkit.UffEvaluationFailure attribute) Construction (cosmolkit.UffEvaluationFailureKind attribute) consumed (cosmolkit.DoubleLexicalReadError property) contact_author (cosmolkit.BioSoftwareItem attribute) contact_author_email (cosmolkit.BioSoftwareItem attribute) contains() (cosmolkit.AvalonFingerprintFlags method) (cosmolkit.CxSmilesFields method) (cosmolkit.LayeredFingerprintLayers method) (cosmolkit.PdbReadFlags method) (cosmolkit.PdbWriteFlags method) (cosmolkit.SanitizeOperations method) Context (cosmolkit.DescriptorSearchCauseKind attribute) context (cosmolkit.PruningError property) Context (cosmolkit.PruningErrorKind attribute) context (cosmolkit.SmartsParseError property) contribs_len (cosmolkit.DescriptorError property) control (cosmolkit.TautomerRunError property) Control (cosmolkit.TautomerRunErrorKind attribute) ControlCCaught (cosmolkit.CipLabelerErrorKind attribute) controlling_atoms (cosmolkit.PotentialStereoInfo attribute) ControllingAtomMismatch (cosmolkit.DoubleBondStereoErrorKind attribute) ControllingSlotOverflow (cosmolkit.DoubleBondStereoErrorKind attribute) converged (cosmolkit.ForceFieldMinimizeOutcome attribute) (cosmolkit.OptimizationOutcome attribute) Converged (cosmolkit.OptimizationStatus attribute) converged_with_energy() (cosmolkit.OptimizationOutcome static method) Conversion (cosmolkit.BioMoleculeErrorKind attribute) conversion (cosmolkit.RequiredPropertyStringError property) Conversion (cosmolkit.RequiredPropertyStringErrorKind attribute) coord_map (cosmolkit.EmbedParams attribute) CoordGenUnavailable (cosmolkit.Coordinate2DErrorKind attribute) coordinate (cosmolkit.ReactionProductError property) Coordinate (cosmolkit.ReactionProductErrorKind attribute) (cosmolkit.TopologyEditErrorKind attribute) (cosmolkit.XyzReadErrorKind attribute) coordinate2_d (cosmolkit.OperationError property) Coordinate2D (cosmolkit.OperationErrorKind attribute) Coordinate2DError Coordinate2DErrorKind (class in cosmolkit) Coordinate2DInputParams (class in cosmolkit) Coordinate2DLayoutError Coordinate2DLayoutErrorKind (class in cosmolkit) Coordinate2DParams (class in cosmolkit) Coordinate2DTemplateError Coordinate2DTemplateErrorKind (class in cosmolkit) Coordinate3DInputParams (class in cosmolkit) Coordinate3DReadError Coordinate3DReadErrorKind (class in cosmolkit) COORDINATE_BONDS (cosmolkit.CxSmilesFields attribute) coordinate_count (cosmolkit.BioStructureError property) coordinate_input (cosmolkit.OperationError property) coordinate_map (cosmolkit.Coordinate2DParams attribute) coordinate_mode (cosmolkit.SdfReadParams attribute) coordinate_rmsd_to() (cosmolkit.Molecule method) coordinate_rmsd_to_with_params() (cosmolkit.Molecule method) coordinate_selection (cosmolkit.CxSmilesWriteParams attribute) (cosmolkit.MolBlockWriteParams attribute) (cosmolkit.PdbWriteParams attribute) (cosmolkit.ReactionProductError property) (cosmolkit.ReactionSingleRunParams attribute) coordinate_selections (cosmolkit.ReactionRunParams attribute) (cosmolkit.ReactionWriteParams attribute) coordinate_validation (cosmolkit.FullCopyComponentError property) (cosmolkit.QueryGraphError property) CoordinateAppendRequiresValues (cosmolkit.OperationErrorKind attribute) CoordinateBlock (class in cosmolkit) (cosmolkit.BioMmcifReadStage attribute) CoordinateBlockSelectionError CoordinateBlockSelectionErrorKind (class in cosmolkit) CoordinateCount (cosmolkit.CxQueryLoweringErrorKind attribute) (cosmolkit.MolecularForceFieldErrorKind attribute) (cosmolkit.SerialConformerOptimizationErrorKind attribute) CoordinateCountMismatch (cosmolkit.BioStructureErrorKind attribute) CoordinateDimension (class in cosmolkit) CoordinateDimensionMismatch (cosmolkit.MolWriteErrorKind attribute) CoordinateGeneration (cosmolkit.DrawingErrorKind attribute) CoordinateInput (cosmolkit.OperationErrorKind attribute) CoordinateInputError CoordinateInputErrorKind (class in cosmolkit) CoordinateMapIndex (cosmolkit.GenerationErrorKind attribute) CoordinateMapNonFinite (cosmolkit.GenerationErrorKind attribute) CoordinateOutOfRange (cosmolkit.SearchMcsErrorKind attribute) CoordinatePlacement (cosmolkit.HydrogenErrorKind attribute) CoordinateRmsdParameters (class in cosmolkit) coordinates (cosmolkit.AlignmentError property) Coordinates (cosmolkit.AttachmentExpansionErrorKind attribute) coordinates (cosmolkit.BioStructure attribute) (cosmolkit.BioStructureParts attribute) (cosmolkit.Conformer2D attribute) (cosmolkit.Conformer3D attribute) (cosmolkit.CoordinateInputError property) Coordinates (cosmolkit.DrawingErrorKind attribute) coordinates (cosmolkit.EnumerationError property) Coordinates (cosmolkit.EnumerationErrorKind attribute) coordinates (cosmolkit.GenerationError property) Coordinates (cosmolkit.GenerationErrorKind attribute) coordinates (cosmolkit.HydrogenError property) (cosmolkit.MatrixError property) Coordinates (cosmolkit.Mol2ReadErrorKind attribute) coordinates (cosmolkit.MoleculeBuilder attribute) Coordinates (cosmolkit.MolProcessingErrorKind attribute) coordinates (cosmolkit.MolWriteError property) Coordinates (cosmolkit.MolWriteErrorKind attribute) (cosmolkit.PdbPostprocessErrorKind attribute) (cosmolkit.PdbWriteErrorKind attribute) (cosmolkit.SdfReadErrorKind attribute) (cosmolkit.SdfWriteErrorKind attribute) coordinates (cosmolkit.SerialCoordinateCountError property) Coordinates (cosmolkit.SmilesParseErrorKind attribute) coordinates (cosmolkit.SmilesStereoError property) Coordinates (cosmolkit.SmilesStereoErrorKind attribute) coordinates (cosmolkit.TautomerRunError property) Coordinates (cosmolkit.TautomerRunErrorKind attribute) coordinates (cosmolkit.UffBuilderError property) (cosmolkit.WedgeError property) Coordinates (cosmolkit.WedgeErrorKind attribute) (cosmolkit.XyzReadErrorKind attribute) (cosmolkit.XyzWriteErrorKind attribute) coordinates_2d (cosmolkit.Molecule attribute) coordinates_3d() (cosmolkit.Molecule method) CoordinateSelection (cosmolkit.ReactionProductErrorKind attribute) CoordinateSelectionArity (cosmolkit.ReactionRunErrorKind attribute) (cosmolkit.ReactionWriteErrorKind attribute) CoordinateShape (cosmolkit.MolecularForceFieldErrorKind attribute) CoordinateValidation (cosmolkit.Coordinate2DErrorKind attribute) (cosmolkit.FullCopyComponentErrorKind attribute) (cosmolkit.QueryGraphErrorKind attribute) CoordinateValidationError CoordinateValidationErrorKind (class in cosmolkit) CoordinateView (cosmolkit.NonbondedFragmentMappingErrorKind attribute) CoordinateZPolicy (class in cosmolkit) COORDS (cosmolkit.CxSmilesFields attribute) Copolymer (cosmolkit.SubstanceGroupKind attribute) copy() (cosmolkit.Molecule method) copy_atom_properties (cosmolkit.ReactionRunParams attribute) CorePropertyString (cosmolkit.UffTypingErrorKind attribute) CoreValence (cosmolkit.UffTypingErrorKind attribute) Corina (cosmolkit.Mol2Type attribute) cosmolkit module count (cosmolkit.AtropisomerError property) (cosmolkit.BioRefinementRestraint attribute) (cosmolkit.Coordinate2DLayoutError property) (cosmolkit.Coordinate3DReadError property) (cosmolkit.CoordinateInputError property) (cosmolkit.McsError property) (cosmolkit.RadicalError property) (cosmolkit.ReactionModelError property) (cosmolkit.ReactionParseError property) (cosmolkit.ReactionRunError property) (cosmolkit.SearchMcsError property) (cosmolkit.SmartsWriteError property) (cosmolkit.SmilesParseError property) (cosmolkit.TautomerRunError property) (cosmolkit.WedgeError property) count_bounds (cosmolkit.AtomPairFingerprintParams attribute) (cosmolkit.AtomPairGeneratorParams attribute) (cosmolkit.MorganFingerprintParams attribute) (cosmolkit.MorganGeneratorParams attribute) (cosmolkit.MorganSettings attribute) (cosmolkit.TopologicalTorsionFingerprintParams attribute) (cosmolkit.TopologicalTorsionGeneratorParams attribute) (cosmolkit.TopologicalTorsionSettings attribute) count_simulation (cosmolkit.AtomPairFingerprintParams attribute) (cosmolkit.AtomPairGeneratorParams attribute) (cosmolkit.MorganFingerprintParams attribute) (cosmolkit.MorganGeneratorParams attribute) (cosmolkit.MorganSettings attribute) (cosmolkit.TopologicalTorsionFingerprintParams attribute) (cosmolkit.TopologicalTorsionGeneratorParams attribute) (cosmolkit.TopologicalTorsionSettings attribute) counter (cosmolkit.PdbLinkRecordError attribute) CounterOutsideSourceIntRange (cosmolkit.PdbSsbondRecordErrorKind attribute) CountLimit (cosmolkit.SdfWriteErrorKind attribute) CountOverflow (cosmolkit.DescriptorErrorKind attribute) Counts (cosmolkit.SdfReadErrorKind attribute) counts() (cosmolkit.MorganFingerprintGenerator method) (cosmolkit.TopologicalTorsionFingerprintGenerator method) Covale (cosmolkit.BioConnectionKind attribute) (cosmolkit.PdbLinkNameCounter attribute) covered (cosmolkit.BioStructureError property) CovRadPauEle (cosmolkit.MmffParamTable attribute) cpci (cosmolkit.EmbedParams attribute) CPS (cosmolkit.ResidueCode attribute) CR (cosmolkit.Element attribute) CR2 (cosmolkit.ResidueCode attribute) CR8 (cosmolkit.ResidueCode attribute) CRF (cosmolkit.ResidueCode attribute) crippen_descriptors() (cosmolkit.Molecule method) crippen_descriptors_with_params() (cosmolkit.Molecule method) CrippenParamNumeric (cosmolkit.DescriptorErrorKind attribute) CrippenTotals (class in cosmolkit) CRO (cosmolkit.ResidueCode attribute) cross_validation_method (cosmolkit.BioRefinementInfo attribute) CrossesDevices (cosmolkit.IoErrorKind attribute) crossing_bond_correspondence (cosmolkit.SubstanceGroup attribute) Crosslink (cosmolkit.SubstanceGroupKind attribute) CRQ (cosmolkit.ResidueCode attribute) CRY (cosmolkit.ResidueCode attribute) crystal (cosmolkit.BioStructure attribute) (cosmolkit.BioStructureParts attribute) (cosmolkit.PdbReaderCause property) Crystal (cosmolkit.PdbReaderCauseKind attribute) CrystalCell (cosmolkit.BioMmcifReadStage attribute) CrystalffTorsionPreferencesError CrystalffTorsionPreferencesErrorKind (class in cosmolkit) crystals (cosmolkit.BioMetadata attribute) CS (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) cs_count (cosmolkit.BioCrystalInfo attribute) CSD (cosmolkit.ResidueCode attribute) CSH (cosmolkit.ResidueCode attribute) CSO (cosmolkit.ResidueCode attribute) CSS (cosmolkit.ResidueCode attribute) cstates (cosmolkit.SubstanceGroup attribute) CSX (cosmolkit.ResidueCode attribute) CU (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) CU1 (cosmolkit.ResidueCode attribute) current (cosmolkit.HydrogenError property) Custom (cosmolkit.AromaticityModel attribute) custom_atom_invariants (cosmolkit.AtomPairFingerprintParams attribute) (cosmolkit.LegacyTopologicalTorsionParams attribute) (cosmolkit.MorganCallParams attribute) (cosmolkit.MorganFingerprintParams attribute) (cosmolkit.TopologicalTorsionCallParams attribute) (cosmolkit.TopologicalTorsionFingerprintParams attribute) custom_bond_invariants (cosmolkit.AtomPairFingerprintParams attribute) (cosmolkit.MorganCallParams attribute) (cosmolkit.MorganFingerprintParams attribute) (cosmolkit.TopologicalTorsionCallParams attribute) (cosmolkit.TopologicalTorsionFingerprintParams attribute) cx (cosmolkit.FragmentCxSmilesWriteParams attribute) Cx (cosmolkit.ReactionWriteErrorKind attribute) cx (cosmolkit.SmilesParseError property) Cx (cosmolkit.SmilesParseErrorKind attribute) cx_fields (cosmolkit.ReactionWriteParams attribute) CxAtomPropertyAtomOutOfRange (cosmolkit.SmilesParseErrorKind attribute) CxAtomPropertyInt (cosmolkit.SmartsWriteErrorKind attribute) CxAtomPropertyKind (cosmolkit.SmartsWriteErrorKind attribute) CxAtomPropertyOutput (cosmolkit.SmartsWriteErrorKind attribute) CxAtomPropertyUInt (cosmolkit.SmartsWriteErrorKind attribute) CxAtomPropertyWrite (cosmolkit.SmartsWriteErrorKind attribute) CxBondConfigAtropMissingCarriers (cosmolkit.SmartsWriteErrorKind attribute) CxBondPropertyUInt (cosmolkit.SmartsWriteErrorKind attribute) CxComposition (cosmolkit.SmartsWriteErrorKind attribute) CxCoordinateAtomOutOfRange (cosmolkit.SmilesParseErrorKind attribute) CxCoordinateOutput (cosmolkit.SmartsWriteErrorKind attribute) CxCoordinates (cosmolkit.SmartsWriteErrorKind attribute) CxCoordinateSelection (class in cosmolkit) (cosmolkit.SmartsWriteErrorKind attribute) CxCoordinateSelectionArity (cosmolkit.SmartsWriteErrorKind attribute) CxCoordinateSource (cosmolkit.SmartsWriteErrorKind attribute) CxCoordinateStorage (cosmolkit.SmartsWriteErrorKind attribute) CXE (cosmolkit.ResidueCode attribute) CxLinkAtomOutOfRange (cosmolkit.SmilesParseErrorKind attribute) CxLinkOrderOutOfRange (cosmolkit.SmilesParseErrorKind attribute) CxLowering (cosmolkit.ReactionParseErrorKind attribute) (cosmolkit.SmartsParseErrorKind attribute) CXM (cosmolkit.ResidueCode attribute) CxMissingConformer (cosmolkit.SmartsWriteErrorKind attribute) CxMissingOutputOrder (cosmolkit.SmartsWriteErrorKind attribute) CxMoleculePropertyUInt (cosmolkit.SmartsWriteErrorKind attribute) CxOutputOrder (cosmolkit.SmartsWriteErrorKind attribute) CxOutputOrderPropertyType (cosmolkit.SmartsWriteErrorKind attribute) CxParse (cosmolkit.ReactionParseErrorKind attribute) CxParseError CxPropertyList (cosmolkit.SmartsWriteErrorKind attribute) CxQueryLoweringError CxQueryLoweringErrorKind (class in cosmolkit) CxRequiredProperty (cosmolkit.SmartsWriteErrorKind attribute) CxRingAtomOrderIndex (cosmolkit.SmartsWriteErrorKind attribute) CxRingInfo (cosmolkit.SmartsWriteErrorKind attribute) CxRingStereoReferenceMissing (cosmolkit.SmartsWriteErrorKind attribute) CxRowCount (cosmolkit.SmartsWriteErrorKind attribute) CxSgroupPropertyUInt (cosmolkit.SmartsWriteErrorKind attribute) CxSgroupPropertyWrite (cosmolkit.SmartsWriteErrorKind attribute) CxSgroupVectorCast (cosmolkit.SmartsWriteErrorKind attribute) CxSmiles (cosmolkit.SmartsParseErrorKind attribute) CxSmilesFields (class in cosmolkit) CxSmilesWriteParams (class in cosmolkit) CxSourceAtomOutOfRange (cosmolkit.SmartsWriteErrorKind attribute) CxSourceBondOutOfRange (cosmolkit.SmartsWriteErrorKind attribute) CxStereoGroup (cosmolkit.SmartsWriteErrorKind attribute) CxStereoGroupMergeError CxStereoGroupMergeErrorKind (class in cosmolkit) CxTypedBondOutOfRange (cosmolkit.SmilesParseErrorKind attribute) CxWedge (cosmolkit.SmartsWriteErrorKind attribute) CxZeroBondOutOfRange (cosmolkit.SmilesParseErrorKind attribute) CyclicPseudoPeptide (cosmolkit.PolymerKind attribute) CYN (cosmolkit.ResidueCode attribute) CYS (cosmolkit.ResidueCode attribute) D DA (cosmolkit.ResidueCode attribute) DAB (cosmolkit.ResidueCode attribute) DAL (cosmolkit.ResidueCode attribute) DAR (cosmolkit.ResidueCode attribute) DAS (cosmolkit.ResidueCode attribute) Data (cosmolkit.SerdeJsonCategory attribute) (cosmolkit.SubstanceGroupKind attribute) data_field() (cosmolkit.SdfRecord method) data_fields (cosmolkit.SdfRecord attribute) data_function (cosmolkit.AtomRangeQuery attribute) database_status (cosmolkit.BioMmcifWriteParams attribute) DataCollection (cosmolkit.BioSoftwareClassification attribute) DataExtraction (cosmolkit.BioSoftwareClassification attribute) DataFieldDouble (cosmolkit.DrawingErrorKind attribute) DataFieldNumber (cosmolkit.MolPostErrorKind attribute) DataLengthMismatch (cosmolkit.PickleErrorKind attribute) DataLengthTooShort (cosmolkit.BoundsMatrixErrorKind attribute) DataProcessing (cosmolkit.BioSoftwareClassification attribute) DataReduction (cosmolkit.BioSoftwareClassification attribute) DataScaling (cosmolkit.BioSoftwareClassification attribute) date (cosmolkit.BioSoftwareItem attribute) DATIVE (cosmolkit.BondOrder attribute) Dative (cosmolkit.BondOrder attribute) DATIVEL (cosmolkit.BondOrder attribute) DativeLeft (cosmolkit.BondOrder attribute) DATIVEONE (cosmolkit.BondOrder attribute) DativeOne (cosmolkit.BondOrder attribute) DATIVER (cosmolkit.BondOrder attribute) DativeRight (cosmolkit.BondOrder attribute) DB (cosmolkit.Element attribute) db_begin (cosmolkit.BioEntityDbRef attribute) db_end (cosmolkit.BioEntityDbRef attribute) db_name (cosmolkit.BioEntityDbRef attribute) db_ref (cosmolkit.PdbReaderCause property) DbRef (cosmolkit.PdbReaderCauseKind attribute) dbrefs (cosmolkit.BioEntityRow attribute) DC (cosmolkit.ResidueCode attribute) DCY (cosmolkit.ResidueCode attribute) DDQ (cosmolkit.ResidueCode attribute) Deadlock (cosmolkit.IoErrorKind attribute) debug_parse (cosmolkit.SmartsParseParams attribute) (cosmolkit.SmilesParseParams attribute) Def (cosmolkit.MmffParamTable attribute) Default (cosmolkit.RotatableBondsOptions attribute) default() (cosmolkit.FingerprintAdditionalOutput static method) (cosmolkit.StereoisomerOptions static method) default_tautomer_score_terms() (in module cosmolkit) DefaultQuery (cosmolkit.UffTorsionBondQueryErrorKind attribute) degenerate (cosmolkit.McsResult attribute) degree (cosmolkit.AtomMetadata attribute) (cosmolkit.CipRankError property) (cosmolkit.DoubleBondStereoError property) (cosmolkit.MoleculeAtom attribute) (cosmolkit.PotentialStereoError property) degree() (cosmolkit.MoleculeBuilder method) DEGREE_PATH (cosmolkit.AvalonFingerprintFlags attribute) DegreeGreaterEqual (cosmolkit.AtomQueryPredicateKind attribute) DegreeLessEqual (cosmolkit.AtomQueryPredicateKind attribute) DenseMatrix (class in cosmolkit) depict (cosmolkit.MolWriteError property) Depict (cosmolkit.MolWriteErrorKind attribute) DerivedEffectContract (cosmolkit.OperationErrorKind attribute) DerivedPreservationMismatch (cosmolkit.OperationErrorKind attribute) description (cosmolkit.BioExperimentalCrystalInfo attribute) (cosmolkit.BioSoftwareItem attribute) (cosmolkit.SmartsWriteError property) descriptor (cosmolkit.PotentialStereoInfo attribute) DescriptorError DescriptorErrorKind (class in cosmolkit) DescriptorListLengthMismatch (cosmolkit.CipLabelerErrorKind attribute) DescriptorNotSupportedForAtoms (cosmolkit.CipLabelerErrorKind attribute) DescriptorNotSupportedForAtropisomerBonds (cosmolkit.CipLabelerErrorKind attribute) DescriptorNotSupportedForDoubleBonds (cosmolkit.CipLabelerErrorKind attribute) DescriptorReadError DescriptorReadErrorKind (class in cosmolkit) DescriptorSearchCause DescriptorSearchCauseKind (class in cosmolkit) DeserializationUnderConstruction (cosmolkit.TautomerCatalogErrorKind attribute) destination (cosmolkit.OperationError property) detached (cosmolkit.MolWriteError property) Detached (cosmolkit.MolWriteErrorKind attribute) detail (cosmolkit.AromaticityError property) (cosmolkit.BioPdbWriteError property) (cosmolkit.CipDescriptorError property) (cosmolkit.CipLabelerError property) (cosmolkit.DescriptorError property) (cosmolkit.FragmentWriteInputError property) Detail (cosmolkit.GraphBoundsErrorKind attribute) detail (cosmolkit.InchiError property) (cosmolkit.KekulizeError property) (cosmolkit.MolecularIoError property) (cosmolkit.OperationError property) (cosmolkit.ReactionProductError property) (cosmolkit.ReactionValidationIssue attribute) (cosmolkit.SmartsParseError property) (cosmolkit.SmartsWriteError property) details (cosmolkit.BioModRes attribute) (cosmolkit.BioTlsSelection attribute) Detect (cosmolkit.BioCoordinateFormat attribute) detect_chemistry_problems() (cosmolkit.Molecule method) detect_chemistry_problems_with_params() (cosmolkit.Molecule method) detector (cosmolkit.BioDiffractionInfo attribute) detector_make (cosmolkit.BioDiffractionInfo attribute) Determined (cosmolkit.BioCalcFlag attribute) dev_ideal (cosmolkit.BioRefinementRestraint attribute) Dfsb (cosmolkit.MmffParamTable attribute) DG (cosmolkit.ResidueCode attribute) dg() (cosmolkit.EmbedParams static method) dg_bounds_matrix() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) dg_bounds_matrix_with_params() (cosmolkit.MoleculeBatch method) DGL (cosmolkit.ResidueCode attribute) DGN (cosmolkit.ResidueCode attribute) DHA (cosmolkit.ResidueCode attribute) DHD (cosmolkit.ResidueCode attribute) DHI (cosmolkit.ResidueCode attribute) DI (cosmolkit.ResidueCode attribute) DIA (cosmolkit.ResidueCode attribute) diagnostics (cosmolkit.InchiResult attribute) Different (cosmolkit.BioAsu attribute) diffraction_ids (cosmolkit.BioExperimentInfo attribute) diffractions (cosmolkit.BioExperimentalCrystalInfo attribute) diffrn (cosmolkit.BioMmcifWriteParams attribute) digit (cosmolkit.PdbChargeError attribute) DIL (cosmolkit.ResidueCode attribute) dimension (cosmolkit.BoundsMatrixError property) (cosmolkit.CoordinateInputError property) (cosmolkit.CoordinateValidationError property) (cosmolkit.DenseMatrix attribute) (cosmolkit.DoubleBondStereoError property) (cosmolkit.HydrogenError property) (cosmolkit.MatrixError property) (cosmolkit.MolWriteError property) (cosmolkit.PdbWriteError property) (cosmolkit.SmilesStereoError property) DimensionOverflow (cosmolkit.BoundsMatrixErrorKind attribute) DIO (cosmolkit.ResidueCode attribute) direction (cosmolkit.Bond attribute) Direction (cosmolkit.BondQueryPredicateKind attribute) direction (cosmolkit.DoubleBondStereoError property) (cosmolkit.MappingValidationError property) (cosmolkit.SmartsWriteError property) direction_code (cosmolkit.Bond attribute) direction_name (cosmolkit.Bond attribute) directions (cosmolkit.SmilesStereoError property) Directions (cosmolkit.SmilesStereoErrorKind attribute) DirectoryNotEmpty (cosmolkit.IoErrorKind attribute) discriminant (cosmolkit.OperationCipStatePolicy attribute) (cosmolkit.OperationMappingRequirement attribute) Dispatch (cosmolkit.UffPreparedOptimizationErrorKind attribute) DispatchedUffOptimizationError DispatchedUffOptimizationErrorKind (class in cosmolkit) display (cosmolkit.SubstanceGroup attribute) display_tag (cosmolkit.SGroupDisplay attribute) distance_matrix() (cosmolkit.Molecule method) distance_matrix_3d() (cosmolkit.Molecule method) distance_matrix_3d_with_params() (cosmolkit.Molecule method) distance_matrix_with_params() (cosmolkit.Molecule method) DistanceMatrix3dParams (class in cosmolkit) DistanceMatrixParams (class in cosmolkit) DistGeomForceFieldError (class in cosmolkit) DistGeomForceFieldErrorKind (class in cosmolkit) Disulf (cosmolkit.BioConnectionKind attribute) DLE (cosmolkit.ResidueCode attribute) DLY (cosmolkit.ResidueCode attribute) DMF (cosmolkit.ResidueCode attribute) DMS (cosmolkit.ResidueCode attribute) DMU (cosmolkit.ResidueCode attribute) DMX (cosmolkit.ResidueCode attribute) DN (cosmolkit.ResidueCode attribute) Dna (cosmolkit.ChainKind attribute) (cosmolkit.PolymerKind attribute) DNA (cosmolkit.ResidueInfoKind attribute) Dna (cosmolkit.ResidueKind attribute) DnaRnaHybrid (cosmolkit.PolymerKind attribute) DOC (cosmolkit.ResidueCode attribute) docs (cosmolkit.FeatureSpec attribute) DOD (cosmolkit.ResidueCode attribute) domain (cosmolkit.AdjacencyError property) (cosmolkit.AdjustHsError property) (cosmolkit.AlignmentError property) (cosmolkit.AromaticityError property) (cosmolkit.AtomCodeError property) (cosmolkit.AtomCodeExplanationError property) (cosmolkit.AtomPairError property) (cosmolkit.AtomPairReadError property) (cosmolkit.AtomPathSubsetCopyError property) (cosmolkit.AtomPropertyError property) (cosmolkit.AtomPropertyReadError property) (cosmolkit.AtropisomerError property) (cosmolkit.AttachmentExpansionError property) (cosmolkit.AutomaticForceFieldConstructionError property) (cosmolkit.AvalonEngineError property) (cosmolkit.AvalonFingerprintError property) (cosmolkit.BatchError property) (cosmolkit.BatchFingerprintOutputError property) (cosmolkit.BatchImageError property) (cosmolkit.BatchValidationError property) (cosmolkit.BioMmcifReadError property) (cosmolkit.BioMmcifWriteError property) (cosmolkit.BioMoleculeConversionError property) (cosmolkit.BioMoleculeError property) (cosmolkit.BioOperationError property) (cosmolkit.BioPdbReadError property) (cosmolkit.BioPdbWriteError property) (cosmolkit.BioReadError property) (cosmolkit.BioRowChainError property) (cosmolkit.BioRowModelError property) (cosmolkit.BioRowTraverseError property) (cosmolkit.BioSelectionCopyCause property) (cosmolkit.BioSelectionCopyError property) (cosmolkit.BioSelectionMatchError property) (cosmolkit.BioSelectionParseError property) (cosmolkit.BioStructureError property) (cosmolkit.BondDirectionStereoError property) (cosmolkit.BondValueError property) (cosmolkit.BoundsMatrixError property) (cosmolkit.BoundsQueryError property) (cosmolkit.CanonicalRankError property) (cosmolkit.ChemCompAtomError property) (cosmolkit.ChemCompModelError property) (cosmolkit.ChemistryProblemError property) (cosmolkit.CifReadError property) (cosmolkit.CipDescriptorError property) (cosmolkit.CipLabelerError property) (cosmolkit.CipRankError property) (cosmolkit.CleanupError property) (cosmolkit.ConformerError property) (cosmolkit.ConformerOptimizerError property) (cosmolkit.ConformerRunError property) (cosmolkit.ConjugationError property) (cosmolkit.Coordinate2DError property) (cosmolkit.Coordinate2DLayoutError property) (cosmolkit.Coordinate2DTemplateError property) (cosmolkit.Coordinate3DReadError property) (cosmolkit.CoordinateBlockSelectionError property) (cosmolkit.CoordinateInputError property) (cosmolkit.CoordinateValidationError property) (cosmolkit.CrystalffTorsionPreferencesError property) (cosmolkit.CxParseError property) (cosmolkit.CxQueryLoweringError property) (cosmolkit.CxStereoGroupMergeError property) (cosmolkit.DescriptorError property) (cosmolkit.DescriptorReadError property) (cosmolkit.DescriptorSearchCause property) (cosmolkit.DispatchedUffOptimizationError property) (cosmolkit.DoubleBondStereoError property) (cosmolkit.DoubleLexicalReadError property) (cosmolkit.DrawingError property) (cosmolkit.DrawingWriteError property) (cosmolkit.EmbedFailureCountError property) (cosmolkit.EmbedSeedError property) (cosmolkit.EnumerationError property) (cosmolkit.EnumerationRunError property) (cosmolkit.ExternalError property) (cosmolkit.FingerprintBatchError property) (cosmolkit.FingerprintError property) (cosmolkit.FingerprintJsonError property) (cosmolkit.FingerprintPreparationError property) (cosmolkit.FingerprintWorkerError property) (cosmolkit.ForceFieldConstructionError property) (cosmolkit.ForceFieldError property) (cosmolkit.ForceFieldKernelError property) (cosmolkit.FragmentCoordinateViewError property) (cosmolkit.FragmentWriteInputError property) (cosmolkit.FromUtf8Error property) (cosmolkit.FullCopyComponentError property) (cosmolkit.GenerationError property) (cosmolkit.GenerationFailure property) (cosmolkit.GraphBoundsError property) (cosmolkit.HybridizationError property) (cosmolkit.HydrogenError property) (cosmolkit.InchiError property) (cosmolkit.IoError property) (cosmolkit.JsonError property) (cosmolkit.KekulizeError property) (cosmolkit.LayeredFingerprintError property) (cosmolkit.LegacyStereoError property) (cosmolkit.MaccsFingerprintError property) (cosmolkit.MappingValidationError property) (cosmolkit.MatchError property) (cosmolkit.MatrixError property) (cosmolkit.McsError property) (cosmolkit.McsProgressError property) (cosmolkit.MissingAtomSiteIdentityField property) (cosmolkit.MissingExplicitHydrogensError property) (cosmolkit.MissingPropertyError property) (cosmolkit.MmcifAssemblyError property) (cosmolkit.MmcifAtomSiteGroupingError property) (cosmolkit.MmcifAtomSiteRowOutOfBounds property) (cosmolkit.MmcifAtomSiteScalarError property) (cosmolkit.MmcifCcdRestoreError property) (cosmolkit.MmcifCisPepError property) (cosmolkit.MmcifConnectionError property) (cosmolkit.MmcifCrystalInfoError property) (cosmolkit.MmcifEntityInfoError property) (cosmolkit.MmcifHelixError property) (cosmolkit.MmcifLabelAddressError property) (cosmolkit.MmcifModResError property) (cosmolkit.MmcifOperationExprError property) (cosmolkit.MmcifSequenceIdError property) (cosmolkit.MmcifSheetError property) (cosmolkit.MmcifSiftsUnpError property) (cosmolkit.MmcifTlsInfoError property) (cosmolkit.MmffAngleLookupError property) (cosmolkit.MmffBuilderError property) (cosmolkit.MmffForceFieldError property) (cosmolkit.MmffMolPropertiesError property) (cosmolkit.MmffOopLookupError property) (cosmolkit.MmffOptimizationError property) (cosmolkit.MmffOptimizationFailure property) (cosmolkit.MmffOptimizationSourceError property) (cosmolkit.MmffParamError property) (cosmolkit.MmffParamParseError property) (cosmolkit.MmffTorLookupError property) (cosmolkit.MmffVdwParseError property) (cosmolkit.MmjsonReadError property) (cosmolkit.MmjsonStructureError property) (cosmolkit.MmjsonValueError property) (cosmolkit.Mol2PostError property) (cosmolkit.Mol2ReadError property) (cosmolkit.MolecularIoError property) (cosmolkit.MoleculeFragmentsError property) (cosmolkit.MoleculeFragmentsFailure property) (cosmolkit.MoleculeHashError property) (cosmolkit.MoleculePropertyError property) (cosmolkit.MoleculeTransferError property) (cosmolkit.MolPostError property) (cosmolkit.MolProcessingError property) (cosmolkit.MolWriteError property) (cosmolkit.MorganError property) (cosmolkit.MorganReadError property) (cosmolkit.NonbondedAssemblyError property) (cosmolkit.NonbondedFragmentMappingError property) (cosmolkit.OperationError property) (cosmolkit.OptimizationStageError property) (cosmolkit.OrderedFragmentBuildError property) (cosmolkit.ParseFloatError property) (cosmolkit.ParserCarrierError property) (cosmolkit.ParserStereoOrderError property) (cosmolkit.PathError property) (cosmolkit.PatternFingerprintError property) (cosmolkit.PdbHeaderError property) (cosmolkit.PdbInputFormatError property) (cosmolkit.PdbModelTransitionError property) (cosmolkit.PdbPostprocessError property) (cosmolkit.PdbReaderCause property) (cosmolkit.PdbRemarkError property) (cosmolkit.PdbResidueKeyError property) (cosmolkit.PdbSsbondResolutionError property) (cosmolkit.PdbWriteError property) (cosmolkit.PeriodicTableError property) (cosmolkit.PickleError property) (cosmolkit.PoisonError property) (cosmolkit.PotentialStereoError property) (cosmolkit.PropertyCacheError property) (cosmolkit.PropertyIntReadError property) (cosmolkit.PropertyStringError property) (cosmolkit.PropertyUIntReadError property) (cosmolkit.PropertyULongReadError property) (cosmolkit.PropertyValueError property) (cosmolkit.ProteinProjectionError property) (cosmolkit.ProteinReadError property) (cosmolkit.PruningError property) (cosmolkit.QueryAtomConversionError property) (cosmolkit.QueryCompileError property) (cosmolkit.QueryGraphError property) (cosmolkit.QueryMatchContextError property) (cosmolkit.QueryStateError property) (cosmolkit.RadicalError property) (cosmolkit.ReactionApplyError property) (cosmolkit.ReactionInitializationError property) (cosmolkit.ReactionModelError property) (cosmolkit.ReactionParseError property) (cosmolkit.ReactionProductError property) (cosmolkit.ReactionRunError property) (cosmolkit.ReactionValidationError property) (cosmolkit.ReactionWriteError property) (cosmolkit.RequiredPropertyStringError property) (cosmolkit.ResidueCodeParseError property) (cosmolkit.ResidueSequenceError property) (cosmolkit.RingDecomposerError property) (cosmolkit.RingFindingError property) (cosmolkit.SanitizeError property) (cosmolkit.ScaffoldError property) (cosmolkit.SdfError property) (cosmolkit.SdfReadError property) (cosmolkit.SdfWriteError property) (cosmolkit.SearchMcsError property) (cosmolkit.SelectedBondCopyError property) (cosmolkit.SelectedSubstanceGroupCopyError property) (cosmolkit.SerdeJsonError property) (cosmolkit.SerialConformerOptimizationError property) (cosmolkit.SerialCoordinateCountError property) (cosmolkit.SerialResultCapacityError property) (cosmolkit.SerialUffOptimizationError property) (cosmolkit.SingleConformerOptimizationError property) (cosmolkit.SmartsParseError property) (cosmolkit.SmartsTraversalError property) (cosmolkit.SmartsWriteError property) (cosmolkit.SmilesError property) (cosmolkit.SmilesParseError property) (cosmolkit.SmilesStereoError property) (cosmolkit.SmilesWriteError property) (cosmolkit.StereoError property) (cosmolkit.StereoGroupError property) (cosmolkit.StereoOrderError property) (cosmolkit.StereoReadError property) (cosmolkit.SubstructMatchError property) (cosmolkit.SvgParseError property) (cosmolkit.TautomerCatalogError property) (cosmolkit.TautomerRunError property) (cosmolkit.TautomerTransformError property) (cosmolkit.TemplateAttachmentOrderError property) (cosmolkit.ThreadCountError property) (cosmolkit.ThreadSelectionError property) (cosmolkit.TopologicalFingerprintError property) (cosmolkit.TopologicalTorsionError property) (cosmolkit.TopologicalTorsionPathScoreError property) (cosmolkit.TopologicalTorsionReadError property) (cosmolkit.TopologyEditError property) (cosmolkit.TopologyValidationError property) (cosmolkit.TransformError property) (cosmolkit.TryReserveError property) (cosmolkit.UffBondMathError property) (cosmolkit.UffBoundsError property) (cosmolkit.UffBuilderError property) (cosmolkit.UffConformerError property) (cosmolkit.UffDefaultTorsionQueryError property) (cosmolkit.UffEvaluationError property) (cosmolkit.UffForceFieldError property) (cosmolkit.UffInversionContributionError property) (cosmolkit.UffOptimizationError property) (cosmolkit.UffParamError property) (cosmolkit.UffParameterError property) (cosmolkit.UffParameterQueryError property) (cosmolkit.UffPreparedOptimizationError property) (cosmolkit.UffSingleError property) (cosmolkit.UffThreadCountError property) (cosmolkit.UffTorsionBondQueryError property) (cosmolkit.UffTypingError property) (cosmolkit.UIntLexicalReadError property) (cosmolkit.UnsignedStreamArrayError property) (cosmolkit.Utf8Error property) (cosmolkit.ValenceError property) (cosmolkit.WedgeError property) (cosmolkit.XmlParseError property) (cosmolkit.XyzReadError property) (cosmolkit.XyzWriteError property) DOUBLE (cosmolkit.BondOrder attribute) Double (cosmolkit.BondOrder attribute) (cosmolkit.PropertyValueKind attribute) Double() (cosmolkit.PropertyValue static method) double_bond (cosmolkit.EnumerationError property) (cosmolkit.LegacyStereoError property) double_bond_stereo (cosmolkit.ReactionProductError property) double_stereo (cosmolkit.CipLabelerError property) DoubleBond (cosmolkit.EnumerationErrorKind attribute) (cosmolkit.LegacyStereoErrorKind attribute) DoubleBondStereo (cosmolkit.MolProcessingErrorKind attribute) (cosmolkit.ReactionProductErrorKind attribute) DoubleBondStereoError DoubleBondStereoErrorKind (class in cosmolkit) DoubleLexicalReadError DoubleLexicalReadErrorKind (class in cosmolkit) DoubleStereo (cosmolkit.CipLabelerErrorKind attribute) (cosmolkit.PotentialStereoErrorKind attribute) DOX (cosmolkit.ResidueCode attribute) dpi_blow_r (cosmolkit.BioRefinementInfo attribute) dpi_blow_rfree (cosmolkit.BioRefinementInfo attribute) dpi_cruickshank_r (cosmolkit.BioRefinementInfo attribute) dpi_cruickshank_rfree (cosmolkit.BioRefinementInfo attribute) DPN (cosmolkit.ResidueCode attribute) DPR (cosmolkit.ResidueCode attribute) DR6 (cosmolkit.ResidueCode attribute) Drawing (cosmolkit.DrawingWriteErrorKind attribute) DrawingError DrawingErrorKind (class in cosmolkit) DrawingWriteError DrawingWriteErrorKind (class in cosmolkit) DS (cosmolkit.Element attribute) DSG (cosmolkit.ResidueCode attribute) DSN (cosmolkit.ResidueCode attribute) DT (cosmolkit.ResidueCode attribute) DtdDetected (cosmolkit.XmlParseErrorKind attribute) DTH (cosmolkit.ResidueCode attribute) DTR (cosmolkit.ResidueCode attribute) DTY (cosmolkit.ResidueCode attribute) DU (cosmolkit.ResidueCode attribute) Dummy (cosmolkit.BioCalcFlag attribute) DUMMY (cosmolkit.Element attribute) duplicate_position (cosmolkit.TemplateAttachmentOrderError property) DuplicateActiveAtom (cosmolkit.MatrixErrorKind attribute) DuplicateActiveBond (cosmolkit.MatrixErrorKind attribute) DuplicateAnisou (cosmolkit.PdbModelTransitionErrorKind attribute) DuplicateAtom (cosmolkit.NonbondedFragmentMappingErrorKind attribute) (cosmolkit.StereoGroupErrorKind attribute) DuplicateBond (cosmolkit.StereoGroupErrorKind attribute) (cosmolkit.TopologyEditErrorKind attribute) DuplicateBondId (cosmolkit.AdjacencyErrorKind attribute) DuplicateBondLigand (cosmolkit.StereoOrderErrorKind attribute) DuplicateCandidateAtom (cosmolkit.KekulizeErrorKind attribute) DuplicateComponentAtom (cosmolkit.CanonicalRankErrorKind attribute) DuplicateConformerId (cosmolkit.CoordinateValidationErrorKind attribute) (cosmolkit.StereoErrorKind attribute) DuplicatedAttribute (cosmolkit.XmlParseErrorKind attribute) DuplicatedNamespace (cosmolkit.XmlParseErrorKind attribute) DuplicateDoneAtom (cosmolkit.KekulizeErrorKind attribute) DuplicateEdge (cosmolkit.AdjacencyErrorKind attribute) (cosmolkit.RingDecomposerErrorKind attribute) DuplicateLabel (cosmolkit.TemplateAttachmentOrderErrorKind attribute) DuplicateModelNumber (cosmolkit.PdbModelTransitionErrorKind attribute) DuplicateName (cosmolkit.CifReadErrorKind attribute) DuplicateProductMap (cosmolkit.ReactionValidationIssueKind attribute) DuplicateReactantMap (cosmolkit.ReactionValidationIssueKind attribute) DuplicateRingBond (cosmolkit.SmartsParseErrorKind attribute) DuplicateSection (cosmolkit.PickleErrorKind attribute) DuplicateTarget (cosmolkit.TemplateAttachmentOrderErrorKind attribute) DVA (cosmolkit.ResidueCode attribute) DXG (cosmolkit.ResidueCode attribute) DY (cosmolkit.Element attribute) E E (cosmolkit.BondStereo attribute) (cosmolkit.CipDescriptor attribute) e (cosmolkit.CipDescriptor attribute) edge (cosmolkit.CipLabelerError property) (cosmolkit.RingFindingError property) EdgeEndpointMismatch (cosmolkit.CipLabelerErrorKind attribute) EdgeNotFound (cosmolkit.RingDecomposerErrorKind attribute) Edit (cosmolkit.AttachmentExpansionErrorKind attribute) edit (cosmolkit.ReactionApplyError property) Edit (cosmolkit.ReactionApplyErrorKind attribute) edit (cosmolkit.ScaffoldError property) Edit (cosmolkit.ScaffoldErrorKind attribute) EditCount (cosmolkit.TautomerRunErrorKind attribute) EDO (cosmolkit.ResidueCode attribute) EEE (cosmolkit.ResidueCode attribute) EffectiveAtomicNumber (cosmolkit.ValencePhase attribute) EGL (cosmolkit.ResidueCode attribute) EigenDecompositionDidNotConverge (cosmolkit.TransformErrorKind attribute) EITHERDOUBLE (cosmolkit.BondDirection attribute) EitherDouble (cosmolkit.BondDirection attribute) Element (class in cosmolkit) element (cosmolkit.Atom attribute) (cosmolkit.BioAtom attribute) (cosmolkit.BioAtomRow attribute) (cosmolkit.ElementInfo attribute) (cosmolkit.MoleculeAtom attribute) (cosmolkit.PeriodicTableError property) (cosmolkit.ProteinAtomRef attribute) element_info() (in module cosmolkit) ElementInfo (class in cosmolkit) elements (cosmolkit.BoundsMatrixError property) Elements (cosmolkit.McsAtomComparator attribute) ElementsLimitReached (cosmolkit.SvgParseErrorKind attribute) ELS (cosmolkit.ResidueInfoKind attribute) embed_3d_conformer_() (cosmolkit.Molecule method) embed_3d_conformer_result_() (cosmolkit.Molecule method) embed_3d_conformer_result_with_params_() (cosmolkit.Molecule method) embed_3d_conformer_with_params_() (cosmolkit.Molecule method) embed_3d_conformers_() (cosmolkit.Molecule method) embed_3d_conformers_result_() (cosmolkit.Molecule method) embed_3d_conformers_result_with_params_() (cosmolkit.Molecule method) embed_3d_conformers_with_params_() (cosmolkit.Molecule method) embed_fragments_separately (cosmolkit.EmbedParams attribute) embedding (cosmolkit.EnumerationError property) Embedding (cosmolkit.EnumerationErrorKind attribute) EmbeddingCoordinates (cosmolkit.EnumerationErrorKind attribute) EmbedFailureCause (class in cosmolkit) EmbedFailureCountError EmbedFailureCountErrorKind (class in cosmolkit) EmbedMoleculeResult (class in cosmolkit) EmbedMultipleConfsResult (class in cosmolkit) EmbedParams (class in cosmolkit) EmbedSeedError EmbedSeedErrorKind (class in cosmolkit) EmbedTermination (class in cosmolkit) Empty (cosmolkit.SdfReadErrorKind attribute) (cosmolkit.TemplateAttachmentOrderErrorKind attribute) (cosmolkit.UIntLexicalReadErrorKind attribute) EmptyAtomMap (cosmolkit.AlignmentErrorKind attribute) EmptyAtomSelection (cosmolkit.SmartsWriteErrorKind attribute) EmptyAttachment (cosmolkit.Coordinate2DLayoutErrorKind attribute) EmptyBlock (cosmolkit.XyzReadErrorKind attribute) EmptyBondSelection (cosmolkit.SmartsWriteErrorKind attribute) EmptyCombinationLevels (cosmolkit.ReactionRunErrorKind attribute) EmptyConfigurationFoci (cosmolkit.CipLabelerErrorKind attribute) EmptyDocument (cosmolkit.CoordinateBlockSelectionErrorKind attribute) EmptyFingerprint (cosmolkit.FingerprintErrorKind attribute) (cosmolkit.PatternFingerprintErrorKind attribute) EmptyFragments (cosmolkit.OperationErrorKind attribute) EmptyGraph (cosmolkit.RingDecomposerErrorKind attribute) EmptyKey (cosmolkit.AtomPropertyErrorKind attribute) (cosmolkit.MoleculePropertyErrorKind attribute) EmptyLine (cosmolkit.UffParamErrorKind attribute) EmptyMolecule (cosmolkit.CrystalffTorsionPreferencesErrorKind attribute) (cosmolkit.MoleculeHashErrorKind attribute) EmptyPairListReference (cosmolkit.CipLabelerErrorKind attribute) EmptyProcessedLine (cosmolkit.MmffParamParseCauseKind attribute) EmptyPropertyKey (cosmolkit.BondValueErrorKind attribute) EmptyRecord (cosmolkit.PdbSsbondRecordErrorKind attribute) EmptyReplacementKey (cosmolkit.SmilesParseErrorKind attribute) EmptyResidueSpan (cosmolkit.BioStructureErrorKind attribute) EmptyRingStereoReferences (cosmolkit.PotentialStereoErrorKind attribute) EmptyTransformMatch (cosmolkit.TautomerRunErrorKind attribute) enable_sequential_random_seeds (cosmolkit.EmbedParams attribute) end (cosmolkit.AdjacencyError property) (cosmolkit.AromaticityError property) (cosmolkit.BioHelix attribute) (cosmolkit.BioRowSpan attribute) (cosmolkit.BioStrand attribute) (cosmolkit.Bond attribute) (cosmolkit.KekulizeError property) (cosmolkit.McsError property) (cosmolkit.MmjsonValueError property) (cosmolkit.QueryGraphError property) (cosmolkit.ReactionParseError property) (cosmolkit.RingFindingError property) (cosmolkit.SubstructMatchError property) (cosmolkit.TopologyEditError property) (cosmolkit.TopologyValidationError property) (cosmolkit.ValenceError property) end_atom (cosmolkit.SmartsParseError property) end_atom_index (cosmolkit.UffTorsionBondQueryError property) end_record (cosmolkit.BioPdbWriteParams attribute) ENDDOWNRIGHT (cosmolkit.BondDirection attribute) EndDownRight (cosmolkit.BondDirection attribute) EndOfEnum (cosmolkit.EmbedFailureCause attribute) endpoint (cosmolkit.AdjacencyError property) (cosmolkit.DoubleBondStereoError property) (cosmolkit.MatrixError property) (cosmolkit.MmcifHelixError property) (cosmolkit.PotentialStereoError property) (cosmolkit.SubstructMatchError property) (cosmolkit.TopologyValidationError property) ENDUPRIGHT (cosmolkit.BondDirection attribute) EndUpRight (cosmolkit.BondDirection attribute) energy (cosmolkit.ForceFieldEnergyGradient attribute) (cosmolkit.ForceFieldMinimizeOutcome attribute) (cosmolkit.MmffEnergyGradient attribute) (cosmolkit.MmffOptimizeMoleculeConfResult attribute) (cosmolkit.MmffOptimizeMoleculeResult attribute) (cosmolkit.OptimizationOutcome attribute) (cosmolkit.UffConformerResult attribute) (cosmolkit.UffEnergyGradient attribute) (cosmolkit.UffOptimizationResult attribute) energy() (cosmolkit.MolecularForceField method) energy_gradient() (cosmolkit.MolecularForceField method) energy_tolerance (cosmolkit.ForceFieldMinimizeParams attribute) enforce_chirality (cosmolkit.EmbedParams attribute) Engine (cosmolkit.AvalonFingerprintErrorKind attribute) ENHANCED_STEREO (cosmolkit.CxSmilesFields attribute) entities (cosmolkit.BioStructure attribute) (cosmolkit.BioStructureParts attribute) entity (cosmolkit.BioMmcifWriteParams attribute) (cosmolkit.MappingValidationError property) (cosmolkit.OperationError property) (cosmolkit.QueryStateError property) (cosmolkit.XmlParseError property) entity_id (cosmolkit.BioChain attribute) (cosmolkit.BioChainRow attribute) (cosmolkit.BioResidue attribute) (cosmolkit.BioResidueRow attribute) (cosmolkit.BioStructureError property) (cosmolkit.MmcifSiftsUnpError property) entity_kind (cosmolkit.BioResidue attribute) (cosmolkit.BioResidueRow attribute) entity_poly (cosmolkit.BioMmcifWriteParams attribute) entity_poly_seq (cosmolkit.BioMmcifWriteParams attribute) EntityKind (class in cosmolkit) EntityNotFound (cosmolkit.MmcifSiftsUnpErrorKind attribute) EntityReferenceLoop (cosmolkit.XmlParseErrorKind attribute) EntityResolver (cosmolkit.XmlParseErrorKind attribute) EntitySequence (cosmolkit.BioMmcifReadStage attribute) EntitySourceIds (class in cosmolkit) EntitySubchainMismatch (cosmolkit.BioStructureErrorKind attribute) entries (cosmolkit.TemplateAttachmentOrder attribute) entries() (cosmolkit.TautomerEnumeration method) (cosmolkit.TautomerProgress method) entry (cosmolkit.BioMmcifWriteParams attribute) entry() (cosmolkit.TautomerProgress method) enumerate_stereoisomers() (cosmolkit.Molecule method) enumerate_stereoisomers_with_options() (cosmolkit.Molecule method) enumerate_stereoisomers_with_random_bits() (cosmolkit.Molecule method) enumerate_tautomers() (cosmolkit.Molecule method) enumerate_tautomers_with_params() (cosmolkit.Molecule method) enumeration (cosmolkit.OperationError property) Enumeration (cosmolkit.OperationErrorKind attribute) EnumerationError EnumerationErrorKind (class in cosmolkit) EnumerationRunError Eof (cosmolkit.SerdeJsonCategory attribute) eof (cosmolkit.SourceNumericStreamState attribute) EOH (cosmolkit.ResidueCode attribute) EPE (cosmolkit.ResidueCode attribute) EqualShortestPathEndpoints (cosmolkit.PathErrorKind attribute) ER (cosmolkit.Element attribute) error (cosmolkit.ChemistryProblem attribute) Error (cosmolkit.CoordinateZPolicy attribute) (cosmolkit.InchiDiagnosticLevel attribute) error (cosmolkit.MmcifCisPepError property) (cosmolkit.MmcifHelixError property) (cosmolkit.MmcifSheetError property) (cosmolkit.MmjsonReadError property) Error (cosmolkit.ReactionValidationSeverity attribute) error_len (cosmolkit.AtomPropertyReadError property) (cosmolkit.Utf8Error property) error_mode (cosmolkit.MoleculeBatch attribute) errors (cosmolkit.BatchExportParams attribute) (cosmolkit.BatchExportReport attribute) (cosmolkit.BatchParams attribute) (cosmolkit.BatchValidationError property) (cosmolkit.MoleculeBatch attribute) (cosmolkit.ReactionValidationReport attribute) ES (cosmolkit.Element attribute) escape (cosmolkit.CrystalffTorsionPreferencesError property) et_version (cosmolkit.EmbedParams attribute) etdg() (cosmolkit.EmbedParams static method) etdg_v2() (cosmolkit.EmbedParams static method) ETF (cosmolkit.ResidueCode attribute) etkdg() (cosmolkit.EmbedParams static method) etkdg_v2() (cosmolkit.EmbedParams static method) etkdg_v3() (cosmolkit.EmbedParams static method) EtkMinimization (cosmolkit.EmbedFailureCause attribute) EU (cosmolkit.Element attribute) Evaluation (cosmolkit.UffOptimizationErrorKind attribute) exact() (cosmolkit.AltLocRequest static method) exact_molecular_weight() (cosmolkit.Molecule method) exact_molecular_weight_with_params() (cosmolkit.Molecule method) ExceededTimeout (cosmolkit.EmbedFailureCause attribute) ExecutableFileBusy (cosmolkit.IoErrorKind attribute) execution (cosmolkit.BatchImageParams attribute) expand_attachment_points (cosmolkit.SdfReadParams attribute) expand_one_letter() (in module cosmolkit) expand_one_letter_sequence() (in module cosmolkit) expected (cosmolkit.AdjustHsError property) (cosmolkit.AromaticityError property) (cosmolkit.AtropisomerError property) (cosmolkit.AttachmentExpansionError property) (cosmolkit.BoundsMatrixError property) (cosmolkit.CanonicalRankError property) (cosmolkit.ConjugationError property) (cosmolkit.CoordinateInputError property) (cosmolkit.CxQueryLoweringError property) (cosmolkit.DescriptorError property) (cosmolkit.DoubleBondStereoError property) (cosmolkit.DrawingError property) (cosmolkit.FingerprintBatchError property) (cosmolkit.ForceFieldError property) (cosmolkit.FragmentCoordinateViewError property) (cosmolkit.FragmentWriteInputError property) (cosmolkit.FullCopyComponentError property) (cosmolkit.HybridizationError property) (cosmolkit.HydrogenError property) (cosmolkit.KekulizeError property) (cosmolkit.MappingValidationError property) (cosmolkit.MmffForceFieldError property) (cosmolkit.MmjsonStructureError property) (cosmolkit.MoleculeTransferError property) (cosmolkit.OperationError property) (cosmolkit.PathError property) (cosmolkit.PdbStructureFinalizationError attribute) (cosmolkit.PickleError property) (cosmolkit.PropertyValueError property) (cosmolkit.QueryMatchContextError property) (cosmolkit.QueryStateError property) (cosmolkit.ReactionRunError property) (cosmolkit.ReactionWriteError property) (cosmolkit.ScaffoldError property) (cosmolkit.SdfError property) (cosmolkit.SdfReadError property) (cosmolkit.SmartsWriteError property) (cosmolkit.SmilesStereoError property) (cosmolkit.TautomerRunError property) (cosmolkit.TopologyEditError property) (cosmolkit.UffBoundsCause attribute) (cosmolkit.UffBuilderError property) (cosmolkit.UffTypingError property) (cosmolkit.XmlParseError property) expected_atoms (cosmolkit.CanonicalRankError property) expected_bonds (cosmolkit.CanonicalRankError property) expected_rows (cosmolkit.DescriptorError property) (cosmolkit.HydrogenError property) expected_start (cosmolkit.BioStructureError property) expected_three_d (cosmolkit.CoordinateValidationError property) expected_two_d (cosmolkit.CoordinateValidationError property) ExpectedArray (cosmolkit.MmjsonStructureErrorKind attribute) ExpectedBondNotFound (cosmolkit.RingFindingErrorKind attribute) ExpectedColon (cosmolkit.JsonErrorKind attribute) ExpectedComma (cosmolkit.JsonErrorKind attribute) ExpectedEndOfInput (cosmolkit.JsonErrorKind attribute) ExpectedFalse (cosmolkit.JsonErrorKind attribute) ExpectedNull (cosmolkit.JsonErrorKind attribute) ExpectedRingBondNotFound (cosmolkit.AromaticityErrorKind attribute) ExpectedTrue (cosmolkit.JsonErrorKind attribute) ExpectedU (cosmolkit.JsonErrorKind attribute) ExpectedValue (cosmolkit.JsonErrorKind attribute) Experimental (cosmolkit.BioMmcifReadStage attribute) (cosmolkit.FunctionStatus attribute) experiments (cosmolkit.BioMetadata attribute) explain_path_score() (in module cosmolkit) explanation (cosmolkit.FunctionStatus attribute) Explicit (cosmolkit.UffPreparedValenceField attribute) explicit (cosmolkit.ValenceError property) Explicit (cosmolkit.ValencePhase attribute) explicit_hydrogens (cosmolkit.Atom attribute) (cosmolkit.MoleculeAtom attribute) (cosmolkit.QueryAtom attribute) explicit_len (cosmolkit.CanonicalRankError property) (cosmolkit.FragmentWriteInputError property) explicit_matrices (cosmolkit.BioCrystalInfo attribute) explicit_only (cosmolkit.AddHsParams attribute) explicit_valence (cosmolkit.AtomMetadata attribute) (cosmolkit.MoleculeAtom attribute) (cosmolkit.ValenceError property) ExplicitDegree (cosmolkit.AtomQueryPredicateKind attribute) (cosmolkit.AtomRangeDataFunctionKind attribute) ExplicitDegreeLessEqual (cosmolkit.AtomQueryPredicateKind attribute) ExplicitHydrogenOverflow (cosmolkit.AdjustHsErrorKind attribute) (cosmolkit.HydrogenErrorKind attribute) ExplicitValence (cosmolkit.AtomQueryPredicateKind attribute) ExplicitValenceCacheNotInitialized (cosmolkit.ValenceErrorKind attribute) exptl (cosmolkit.BioMmcifWriteParams attribute) ExternalError ExternalInvalidSmarts (cosmolkit.Coordinate2DTemplateErrorKind attribute) ExternalOpen (cosmolkit.Coordinate2DTemplateErrorKind attribute) ExternalRead (cosmolkit.Coordinate2DTemplateErrorKind attribute) extra_atom_check (cosmolkit.SubstructMatchParams attribute) extra_atom_check_overrides_default_check (cosmolkit.SubstructMatchParams attribute) extra_bond_check (cosmolkit.SubstructMatchParams attribute) extra_bond_check_overrides_default_check (cosmolkit.SubstructMatchParams attribute) extra_final_check (cosmolkit.SubstructMatchParams attribute) ExtraInvariantLength (cosmolkit.PathErrorKind attribute) F F (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) factor (cosmolkit.FingerprintError property) FAD (cosmolkit.ResidueCode attribute) fail (cosmolkit.SourceNumericStreamState attribute) failed (cosmolkit.BatchExportReport attribute) failure (cosmolkit.MoleculeFragmentsError property) (cosmolkit.UffEvaluationError property) failure_count() (cosmolkit.EmbedMoleculeResult method) (cosmolkit.EmbedMultipleConfsResult method) failure_counts (cosmolkit.EmbedMoleculeResult attribute) (cosmolkit.EmbedMultipleConfsResult attribute) failures (cosmolkit.EmbedParams attribute) failures_tracked (cosmolkit.EmbedMoleculeResult attribute) (cosmolkit.EmbedMultipleConfsResult attribute) False_ (cosmolkit.MmjsonUnexpectedType attribute) fasta_code (cosmolkit.ProteinResidueRef attribute) (cosmolkit.ResidueInfo attribute) FastSubset (cosmolkit.OrderedFragmentBuildErrorKind attribute) FCY (cosmolkit.ResidueCode attribute) FE (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) FE2 (cosmolkit.ResidueCode attribute) feature (cosmolkit.Mol2ReadError property) (cosmolkit.ParityMatrixEntry attribute) (cosmolkit.PdbWriteError property) (cosmolkit.SmartsParseError property) (cosmolkit.SupportMatrixEntry attribute) (cosmolkit.UnsupportedFeatureError attribute) FEATURE_PAIRS (cosmolkit.AvalonFingerprintFlags attribute) feature_spec() (in module cosmolkit) feature_specs() (in module cosmolkit) FeaturePatterns() (cosmolkit.MorganInvariants static method) Features (cosmolkit.MorganInvariants attribute) features() (cosmolkit.MorganAtomInvariantsGenerator static method) FeatureSpec (class in cosmolkit) FeatureSpecIter (class in cosmolkit) FGA (cosmolkit.ResidueCode attribute) field (cosmolkit.AdjustHsError property) (cosmolkit.AromaticityError property) (cosmolkit.BioMmcifWriteError property) (cosmolkit.BioPdbWriteError property) (cosmolkit.CipRankError property) (cosmolkit.ConjugationError property) (cosmolkit.DescriptorError property) (cosmolkit.DrawingError property) (cosmolkit.HybridizationError property) (cosmolkit.HydrogenError property) (cosmolkit.KekulizeError property) (cosmolkit.MissingAtomSiteIdentityField property) (cosmolkit.MolPostError property) (cosmolkit.OperationError property) (cosmolkit.PdbStructureFinalizationError attribute) (cosmolkit.PotentialStereoError property) (cosmolkit.QueryMatchContextError property) (cosmolkit.RadicalError property) (cosmolkit.ScaffoldError property) Field (cosmolkit.SdfReadErrorKind attribute) field (cosmolkit.SmilesStereoError property) (cosmolkit.StereoError property) (cosmolkit.TautomerRunError property) (cosmolkit.TopologicalFingerprintError property) (cosmolkit.UffBoundsCause attribute) (cosmolkit.UffBuilderError property) (cosmolkit.ValenceError property) field_offset (cosmolkit.PdbConectError attribute) (cosmolkit.PdbCrystalError attribute) (cosmolkit.PdbDbRefError attribute) (cosmolkit.PdbHeaderError property) (cosmolkit.PdbHelixError attribute) (cosmolkit.PdbModResError attribute) (cosmolkit.PdbMtrixError attribute) (cosmolkit.PdbRemark350Error attribute) (cosmolkit.PdbSheetError attribute) field_position (cosmolkit.SGroupDisplay attribute) fields (cosmolkit.CxSmilesWriteParams attribute) filenames (cosmolkit.BatchImageParams attribute) FileTooLarge (cosmolkit.IoErrorKind attribute) FileWrite (cosmolkit.BioMmcifWriteErrorKind attribute) final_match (cosmolkit.SubstructMatchParams attribute) FinalCenterInVolume (cosmolkit.EmbedFailureCause attribute) FinalCheckBondEndpoint (cosmolkit.SubstructMatchErrorKind attribute) FinalCheckInvariant (cosmolkit.SubstructMatchErrorKind attribute) FinalCheckMappingIndex (cosmolkit.SubstructMatchErrorKind attribute) FinalCheckMappingLength (cosmolkit.SubstructMatchErrorKind attribute) FinalCheckMissingBond (cosmolkit.SubstructMatchErrorKind attribute) FinalChiralBounds (cosmolkit.EmbedFailureCause attribute) FinalComputedProperties (cosmolkit.MoleculeFragmentsFailureKind attribute) FinalEnergy (cosmolkit.OptimizationStageErrorKind attribute) Finalization (cosmolkit.BioPdbReadStage attribute) finalization (cosmolkit.PdbReaderCause property) Finalization (cosmolkit.PdbReaderCauseKind attribute) FinalSanitize (cosmolkit.MoleculeFragmentsFailureKind attribute) find_atom() (cosmolkit.BioStructure method) find_chiral_centers() (cosmolkit.Molecule method) find_entity() (cosmolkit.BioStructure method) find_entity_of_subchain() (cosmolkit.BioStructure method) FIND_RADICALS (cosmolkit.SanitizeOperations attribute) find_residue_info() (in module cosmolkit) find_residue_info_index() (in module cosmolkit) FindRadicals (cosmolkit.SanitizeStage attribute) Fingerprint (class in cosmolkit) (cosmolkit.AtomPairErrorKind attribute) fingerprint (cosmolkit.BatchFingerprintOutput attribute) (cosmolkit.LayeredFingerprintResult attribute) Fingerprint (cosmolkit.MorganErrorKind attribute) fingerprint (cosmolkit.TopologicalFingerprintResult attribute) Fingerprint (cosmolkit.TopologicalTorsionErrorKind attribute) fingerprint_atom_pair() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) fingerprint_atom_pair_count() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) fingerprint_atom_pair_count_with_params() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) fingerprint_atom_pair_sparse() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) fingerprint_atom_pair_sparse_count() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) fingerprint_atom_pair_sparse_count_with_params() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) fingerprint_atom_pair_sparse_with_params() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) fingerprint_atom_pair_with_output() (cosmolkit.MoleculeBatch method) fingerprint_atom_pair_with_output_with_params() (cosmolkit.MoleculeBatch method) fingerprint_atom_pair_with_params() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) fingerprint_avalon() (cosmolkit.Molecule method) fingerprint_avalon_with_params() (cosmolkit.Molecule method) fingerprint_kind (cosmolkit.BatchFingerprintOutputError property) fingerprint_layered() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) fingerprint_layered_query_with_output_with_params() (in module cosmolkit) fingerprint_layered_query_with_params() (in module cosmolkit) fingerprint_layered_with_output() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) fingerprint_layered_with_output_with_params() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) fingerprint_layered_with_params() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) fingerprint_maccs() (cosmolkit.Molecule method) fingerprint_maccs_raw() (cosmolkit.Molecule method) fingerprint_maccs_with_params() (cosmolkit.Molecule method) fingerprint_morgan() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) fingerprint_morgan_count() (cosmolkit.Molecule method) fingerprint_morgan_count_with_generator() (cosmolkit.Molecule method) fingerprint_morgan_count_with_params() (cosmolkit.Molecule method) fingerprint_morgan_sparse() (cosmolkit.Molecule method) fingerprint_morgan_sparse_count() (cosmolkit.Molecule method) fingerprint_morgan_sparse_count_with_generator() (cosmolkit.Molecule method) fingerprint_morgan_sparse_count_with_params() (cosmolkit.Molecule method) fingerprint_morgan_sparse_with_generator() (cosmolkit.Molecule method) fingerprint_morgan_sparse_with_params() (cosmolkit.Molecule method) fingerprint_morgan_with_generator() (cosmolkit.Molecule method) fingerprint_morgan_with_generator_params() (cosmolkit.MoleculeBatch method) fingerprint_morgan_with_output() (cosmolkit.MoleculeBatch method) fingerprint_morgan_with_output_with_generator_params() (cosmolkit.MoleculeBatch method) fingerprint_morgan_with_output_with_params() (cosmolkit.MoleculeBatch method) fingerprint_morgan_with_params() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) fingerprint_pattern() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) fingerprint_pattern_query() (in module cosmolkit) fingerprint_pattern_query_with_params() (in module cosmolkit) fingerprint_pattern_with_params() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) fingerprint_topological() (cosmolkit.Molecule method) fingerprint_topological_query_with_output_with_params() (in module cosmolkit) fingerprint_topological_query_with_params() (in module cosmolkit) fingerprint_topological_torsion() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) fingerprint_topological_torsion_count() (cosmolkit.Molecule method) fingerprint_topological_torsion_count_legacy() (cosmolkit.Molecule method) fingerprint_topological_torsion_count_legacy_with_params() (cosmolkit.Molecule method) fingerprint_topological_torsion_count_with_generator() (cosmolkit.Molecule method) fingerprint_topological_torsion_count_with_params() (cosmolkit.Molecule method) fingerprint_topological_torsion_legacy() (cosmolkit.Molecule method) fingerprint_topological_torsion_legacy_with_params() (cosmolkit.Molecule method) fingerprint_topological_torsion_sparse() (cosmolkit.Molecule method) fingerprint_topological_torsion_sparse_count() (cosmolkit.Molecule method) fingerprint_topological_torsion_sparse_count_legacy() (cosmolkit.Molecule method) fingerprint_topological_torsion_sparse_count_legacy_with_params() (cosmolkit.Molecule method) fingerprint_topological_torsion_sparse_count_with_generator() (cosmolkit.Molecule method) fingerprint_topological_torsion_sparse_count_with_params() (cosmolkit.Molecule method) fingerprint_topological_torsion_sparse_with_generator() (cosmolkit.Molecule method) fingerprint_topological_torsion_sparse_with_params() (cosmolkit.Molecule method) fingerprint_topological_torsion_with_generator() (cosmolkit.Molecule method) fingerprint_topological_torsion_with_params() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) fingerprint_topological_with_output() (cosmolkit.Molecule method) fingerprint_topological_with_output_with_params() (cosmolkit.Molecule method) fingerprint_topological_with_params() (cosmolkit.Molecule method) FingerprintAdditionalOutput (class in cosmolkit) FingerprintBatch (class in cosmolkit) FingerprintBatchError FingerprintBatchErrorKind (class in cosmolkit) FingerprintError FingerprintErrorKind (class in cosmolkit) FingerprintJsonError FingerprintJsonErrorKind (class in cosmolkit) FingerprintPreparationError FingerprintPreparationErrorKind (class in cosmolkit) fingerprints() (cosmolkit.MorganFingerprintGenerator method) (cosmolkit.TopologicalTorsionFingerprintGenerator method) FingerprintWorkerError FingerprintWorkerErrorKind (class in cosmolkit) first (cosmolkit.Coordinate2DLayoutError property) First (cosmolkit.ForceFieldAngleIndexArgument attribute) (cosmolkit.ForceFieldBondIndexArgument attribute) (cosmolkit.ForceFieldTorsionIndexArgument attribute) first (cosmolkit.StereoOrderError property) (cosmolkit.TransformError property) First (cosmolkit.UffInversionIndexArgument attribute) first_bond (cosmolkit.AdjacencyError property) (cosmolkit.TransformError property) first_component (cosmolkit.NonbondedFragmentMappingError property) first_mon() (cosmolkit.BioEntityRow static method) first_position (cosmolkit.AdjacencyError property) (cosmolkit.MatrixError property) (cosmolkit.TemplateAttachmentOrderError property) first_role (cosmolkit.TransformError property) FirstMinimization (cosmolkit.EmbedFailureCause attribute) FIVEANDAHALF (cosmolkit.BondOrder attribute) FiveAndHalf (cosmolkit.BondOrder attribute) fixed_atoms (cosmolkit.MolecularForceField attribute) FL (cosmolkit.Element attribute) flag (cosmolkit.ReactionParseError property) flag_possible (cosmolkit.PotentialStereoParams attribute) flavor (cosmolkit.BioMoleculeParams attribute) (cosmolkit.PdbWriteParams attribute) flips_per_sample (cosmolkit.Coordinate2DParams attribute) FLO (cosmolkit.ResidueCode attribute) FloatingEnvironmentNotModeled (cosmolkit.DoubleLexicalReadErrorKind attribute) FM (cosmolkit.Element attribute) FME (cosmolkit.ResidueCode attribute) FMN (cosmolkit.ResidueCode attribute) FMT (cosmolkit.ResidueCode attribute) force_2d (cosmolkit.MolBlockWriteParams attribute) force_constant (cosmolkit.ForceFieldAngleConstraintParams attribute) (cosmolkit.ForceFieldDistanceConstraintParams attribute) (cosmolkit.ForceFieldPositionConstraintParams attribute) (cosmolkit.ForceFieldTorsionConstraintParams attribute) force_field (cosmolkit.GenerationError property) force_field_kernel (cosmolkit.MmffBuilderError property) force_rdkit (cosmolkit.Coordinate2DParams attribute) force_tolerance (cosmolkit.ForceFieldMinimizeParams attribute) force_trans_amides (cosmolkit.EmbedParams attribute) ForceField (cosmolkit.GenerationErrorKind attribute) ForceFieldAngleConstraintParams (class in cosmolkit) ForceFieldAngleIndexArgument (class in cosmolkit) ForceFieldAngleRangeBound (class in cosmolkit) ForceFieldBondIndexArgument (class in cosmolkit) ForceFieldConstructionError ForceFieldConstructionErrorKind (class in cosmolkit) ForceFieldDistanceConstraintParams (class in cosmolkit) ForceFieldEnergyGradient (class in cosmolkit) ForceFieldError ForceFieldIndexArgument (class in cosmolkit) ForceFieldKernel (cosmolkit.MmffBuilderErrorKind attribute) (cosmolkit.UffBuilderErrorKind attribute) ForceFieldKernelError ForceFieldKernelErrorKind (class in cosmolkit) ForceFieldMinimizeOutcome (class in cosmolkit) ForceFieldMinimizeParams (class in cosmolkit) ForceFieldPositionConstraintParams (class in cosmolkit) ForceFieldTorsionConstraintParams (class in cosmolkit) ForceFieldTorsionIndexArgument (class in cosmolkit) formal_charge (cosmolkit.Atom attribute) (cosmolkit.BioAtom attribute) (cosmolkit.BioAtomRow attribute) (cosmolkit.MmffAtomProperties attribute) (cosmolkit.MoleculeAtom attribute) (cosmolkit.QueryAtom attribute) (cosmolkit.ValenceError property) formal_charge() (cosmolkit.MmffProperties method) FormalCharge (cosmolkit.AtomQueryPredicateKind attribute) (cosmolkit.AtomRangeDataFunctionKind attribute) FormalChargeOutOfRange (cosmolkit.TautomerRunErrorKind attribute) format (cosmolkit.BatchExportParams attribute) (cosmolkit.BatchImageError property) (cosmolkit.BatchImageParams attribute) (cosmolkit.BioReadError property) (cosmolkit.BioReadParams attribute) (cosmolkit.MolBlockWriteParams attribute) (cosmolkit.MolecularIoError property) (cosmolkit.SdfReadError property) Formulation (cosmolkit.SubstanceGroupKind attribute) found (cosmolkit.ResidueInfo attribute) FOURANDAHALF (cosmolkit.BondOrder attribute) FourAndHalf (cosmolkit.BondOrder attribute) Fourth (cosmolkit.ForceFieldTorsionIndexArgument attribute) (cosmolkit.UffInversionIndexArgument attribute) fp_size (cosmolkit.AtomPairFingerprintParams attribute) (cosmolkit.AtomPairGeneratorParams attribute) (cosmolkit.LayeredFingerprintParams attribute) (cosmolkit.LegacyTopologicalTorsionParams attribute) (cosmolkit.MorganFingerprintParams attribute) (cosmolkit.MorganGeneratorParams attribute) (cosmolkit.MorganSettings attribute) (cosmolkit.TopologicalFingerprintParams attribute) (cosmolkit.TopologicalTorsionFingerprintParams attribute) (cosmolkit.TopologicalTorsionGeneratorParams attribute) (cosmolkit.TopologicalTorsionSettings attribute) FR (cosmolkit.Element attribute) fraction (cosmolkit.BioAtom attribute) (cosmolkit.BioAtomRow attribute) fraction_csp3() (cosmolkit.Molecule method) fractional (cosmolkit.BioCrystalInfo attribute) FractionalTransform (cosmolkit.BioMmcifReadStage attribute) Fragment (cosmolkit.Coordinate2DErrorKind attribute) fragment (cosmolkit.MmffBuilderError property) Fragment (cosmolkit.MmffBuilderErrorKind attribute) (cosmolkit.SmilesWriteErrorKind attribute) fragment_count (cosmolkit.FragmentWriteInputError property) FragmentAtomOutOfRange (cosmolkit.SmartsWriteErrorKind attribute) FragmentBondOutOfRange (cosmolkit.SmartsWriteErrorKind attribute) FragmentCoordinateViewError FragmentCoordinateViewErrorKind (class in cosmolkit) FragmentCopy (cosmolkit.NonbondedFragmentMappingErrorKind attribute) FragmentCxSmilesWriteParams (class in cosmolkit) FragmentMapping (cosmolkit.NonbondedAssemblyErrorKind attribute) fragments (cosmolkit.GenerationError property) Fragments (cosmolkit.GenerationErrorKind attribute) fragments (cosmolkit.OperationError property) Fragments (cosmolkit.OperationErrorKind attribute) fragments() (cosmolkit.Molecule method) FragmentSmilesWriteParams (class in cosmolkit) FragmentWriteInputError FragmentWriteInputErrorKind (class in cosmolkit) from_ (cosmolkit.BioPdbWriteError property) (cosmolkit.RingDecomposerError property) from_ascii() (cosmolkit.AtomName static method) from_atomic_number() (cosmolkit.Element static method) from_atoms (cosmolkit.AtomPairFingerprintParams attribute) (cosmolkit.LayeredFingerprintParams attribute) (cosmolkit.LegacyTopologicalTorsionParams attribute) (cosmolkit.MorganCallParams attribute) (cosmolkit.MorganFingerprintParams attribute) (cosmolkit.TopologicalFingerprintParams attribute) (cosmolkit.TopologicalTorsionCallParams attribute) (cosmolkit.TopologicalTorsionFingerprintParams attribute) from_binary() (cosmolkit.Molecule static method) from_bits() (cosmolkit.AvalonFingerprintFlags static method) (cosmolkit.PdbReadFlags static method) (cosmolkit.PdbWriteFlags static method) (cosmolkit.SanitizeOperations static method) from_bits_retain() (cosmolkit.AvalonFingerprintFlags static method) (cosmolkit.LayeredFingerprintLayers static method) from_cid() (cosmolkit.BioSelection static method) from_code() (cosmolkit.AtomCodeExplanation static method) from_dataset_indices() (cosmolkit.MoleculeBatch static method) from_inchi() (cosmolkit.Molecule static method) from_inchi_with_params() (cosmolkit.Molecule static method) from_integer_seed() (cosmolkit.StereoisomerRandomSource static method) from_json() (cosmolkit.MorganFingerprintGenerator static method) (cosmolkit.TopologicalTorsionFingerprintGenerator static method) from_mmcif() (cosmolkit.BioStructure static method) (cosmolkit.Molecule static method) (cosmolkit.Protein static method) from_mmcif_with_params() (cosmolkit.Molecule static method) from_mol() (cosmolkit.Molecule static method) from_mol2() (cosmolkit.Molecule static method) from_mol2_with_params() (cosmolkit.Molecule static method) from_mol_with_params() (cosmolkit.Molecule static method) from_name() (cosmolkit.CoordinateZPolicy static method) from_on_bits() (cosmolkit.Fingerprint static method) from_parts() (cosmolkit.BioStructure static method) (cosmolkit.Molecule static method) (cosmolkit.MoleculeBuilder static method) from_pdb() (cosmolkit.BioStructure static method) (cosmolkit.Molecule static method) (cosmolkit.Protein static method) from_pdb_with_params() (cosmolkit.BioStructure static method) (cosmolkit.Molecule static method) (cosmolkit.Protein static method) from_query_graph() (cosmolkit.SdfRecord static method) from_random_bits() (cosmolkit.StereoisomerRandomSource static method) from_rdkit() (cosmolkit.Molecule static method) from_records() (cosmolkit.MoleculeBatch static method) from_sdf() (cosmolkit.Molecule static method) (cosmolkit.SdfRecord static method) from_sdf_records() (cosmolkit.MoleculeBatch static method) from_sdf_records_with_params() (cosmolkit.MoleculeBatch static method) from_sdf_with_params() (cosmolkit.Molecule static method) (cosmolkit.SdfRecord static method) from_smarts() (cosmolkit.QueryGraph static method) from_smarts_with_params() (cosmolkit.QueryGraph static method) from_smiles() (cosmolkit.Molecule static method) from_smiles_list() (cosmolkit.MoleculeBatch static method) from_smiles_list_with_params() (cosmolkit.MoleculeBatch static method) from_smiles_with_params() (cosmolkit.Molecule static method) from_smirks() (cosmolkit.Reaction static method) from_smirks_with_params() (cosmolkit.Reaction static method) from_symbol() (cosmolkit.Element static method) from_templates() (cosmolkit.Reaction static method) from_text() (cosmolkit.BioStructure static method) (cosmolkit.Protein static method) from_text_with_params() (cosmolkit.BioStructure static method) (cosmolkit.Protein static method) from_transform_data() (cosmolkit.TautomerParams static method) from_transform_file() (cosmolkit.TautomerParams static method) from_usize() (cosmolkit.BioRowSpan static method) from_xyz_block() (cosmolkit.Molecule static method) FromUtf8Error frontier (cosmolkit.SearchMcsError property) FRU (cosmolkit.ResidueCode attribute) fsc_free (cosmolkit.BioBasicRefinementInfo attribute) fsc_work (cosmolkit.BioBasicRefinementInfo attribute) FUC (cosmolkit.ResidueCode attribute) full_sequence (cosmolkit.BioEntityRow attribute) FullCopyComponentError FullCopyComponentErrorKind (class in cosmolkit) function (cosmolkit.BioRefinementRestraint attribute) (cosmolkit.DescriptorError property) FunctionStatus (class in cosmolkit) fuzzy_and() (cosmolkit.SparseCountFingerprint method) (cosmolkit.SparseCountFingerprint32 method) fuzzy_or() (cosmolkit.SparseCountFingerprint method) (cosmolkit.SparseCountFingerprint32 method) FVA (cosmolkit.ResidueCode attribute) G G (cosmolkit.ResidueCode attribute) GA (cosmolkit.Element attribute) GAL (cosmolkit.ResidueCode attribute) gamma (cosmolkit.BioCrystalCell attribute) GBL (cosmolkit.ResidueCode attribute) GCD (cosmolkit.ResidueCode attribute) GD (cosmolkit.Element attribute) GDP (cosmolkit.ResidueCode attribute) GE (cosmolkit.Element attribute) generated_count (cosmolkit.EmbedMultipleConfsResult attribute) generation_failed (cosmolkit.GenerationError property) GenerationError GenerationErrorKind (class in cosmolkit) GenerationFailed (cosmolkit.ConformerErrorKind attribute) (cosmolkit.GenerationErrorKind attribute) GenerationFailure GenerationFailureKind (class in cosmolkit) Generator (cosmolkit.AtomPairReadErrorKind attribute) (cosmolkit.MorganReadErrorKind attribute) (cosmolkit.TopologicalTorsionReadErrorKind attribute) generators (cosmolkit.BioAssembly attribute) Generic() (cosmolkit.SubstanceGroupKind static method) generic_value (cosmolkit.SubstanceGroupKind attribute) geometry (cosmolkit.WedgeError property) Geometry (cosmolkit.WedgeErrorKind attribute) GeometryNotEnoughNeighbors (cosmolkit.Coordinate2DLayoutErrorKind attribute) get() (cosmolkit.DenseMatrix method) (cosmolkit.MoleculeBatch method) (cosmolkit.TautomerEnumeration method) get_bit() (cosmolkit.Fingerprint method) getter (cosmolkit.QueryMatchContextError property) GHP (cosmolkit.ResidueCode attribute) given (cosmolkit.BioNcsOperator attribute) GL3 (cosmolkit.ResidueCode attribute) GLA (cosmolkit.ResidueCode attribute) GLC (cosmolkit.ResidueCode attribute) GLN (cosmolkit.ResidueCode attribute) GLO (cosmolkit.ResidueCode attribute) GLU (cosmolkit.ResidueCode attribute) GLX (cosmolkit.ResidueCode attribute) GLY (cosmolkit.ResidueCode attribute) GOL (cosmolkit.ResidueCode attribute) GPX (cosmolkit.ResidueCode attribute) gradient (cosmolkit.ForceFieldEnergyGradient attribute) (cosmolkit.MmffEnergyGradient attribute) (cosmolkit.UffEnergyGradient attribute) gradient() (cosmolkit.MolecularForceField method) gradient_unconstrained() (cosmolkit.MolecularForceField method) Graft (cosmolkit.SubstanceGroupKind attribute) graph (cosmolkit.SdfRecord attribute) GraphBoundsError GraphBoundsErrorKind (class in cosmolkit) GraphDistance (cosmolkit.Coordinate2DLayoutErrorKind attribute) GraphPath (cosmolkit.Coordinate2DLayoutErrorKind attribute) GreaterEqual (cosmolkit.AtomRangeBoundsKind attribute) group (cosmolkit.DrawingError property) (cosmolkit.MolPostError property) (cosmolkit.SdfWriteError property) (cosmolkit.SelectedSubstanceGroupCopyError property) (cosmolkit.SmartsWriteError property) (cosmolkit.TopologyEditError property) group_pdb (cosmolkit.BioMmcifWriteParams attribute) groups (cosmolkit.CxStereoGroupMergeError property) GYS (cosmolkit.ResidueCode attribute) H H (cosmolkit.Element attribute) H2U (cosmolkit.ResidueCode attribute) hall_kier_alpha() (cosmolkit.Molecule method) hall_kier_alpha_with_contributions() (cosmolkit.Molecule method) HanoiScratchTooSmall (cosmolkit.CanonicalRankErrorKind attribute) has_2d_coordinates (cosmolkit.Molecule attribute) has_d_fraction (cosmolkit.BioStructureSourceState attribute) has_origx (cosmolkit.BioStructure attribute) (cosmolkit.BioStructureSourceState attribute) has_substruct_match() (cosmolkit.Molecule method) has_substruct_match_with_params() (cosmolkit.Molecule method) has_valence_violation() (cosmolkit.Molecule method) HasAliphaticHeteroatomNeighbors (cosmolkit.AtomQueryPredicateKind attribute) HasChiralTag (cosmolkit.AtomQueryPredicateKind attribute) hashes (cosmolkit.CxStereoGroupMergeError property) HasHeteroatomNeighbors (cosmolkit.AtomQueryPredicateKind attribute) HasImplicitHydrogen (cosmolkit.AtomQueryPredicateKind attribute) HasProperty (cosmolkit.AtomQueryPredicateKind attribute) (cosmolkit.BondQueryPredicateKind attribute) HasRingBond (cosmolkit.AtomQueryPredicateKind attribute) HasStereo (cosmolkit.BondQueryPredicateKind attribute) hbond_atom1 (cosmolkit.BioStrand attribute) hbond_atom2 (cosmolkit.BioStrand attribute) HCOUNT_CLASS_PATH (cosmolkit.AvalonFingerprintFlags attribute) HCOUNT_PAIR (cosmolkit.AvalonFingerprintFlags attribute) HCOUNT_PATH (cosmolkit.AvalonFingerprintFlags attribute) HE (cosmolkit.Element attribute) head_crossing_bonds (cosmolkit.SubstanceGroup attribute) header (cosmolkit.PdbReaderCause property) Header (cosmolkit.PdbReaderCauseKind attribute) HeavyAtomDegree (cosmolkit.AtomQueryPredicateKind attribute) height (cosmolkit.BatchImageParams attribute) (cosmolkit.DrawingError property) Helices (cosmolkit.BioMmcifReadStage attribute) helices (cosmolkit.BioStructure attribute) (cosmolkit.BioStructureParts attribute) helix (cosmolkit.PdbReaderCause property) Helix (cosmolkit.PdbReaderCauseKind attribute) Helix27 (cosmolkit.BioHelixClass attribute) HelixClass (cosmolkit.MmcifHelixErrorKind attribute) HelixLength (cosmolkit.MmcifHelixErrorKind attribute) HelixPolyProlineNone (cosmolkit.BioHelixClass attribute) HEM (cosmolkit.ResidueCode attribute) HerschbachLaurie (cosmolkit.MmffParamTable attribute) het_flag (cosmolkit.BioResidue attribute) (cosmolkit.BioResidueRow attribute) hetero_hydrogen (cosmolkit.TautomerScore attribute) HEXTUPLE (cosmolkit.BondOrder attribute) Hextuple (cosmolkit.BondOrder attribute) HEZ (cosmolkit.ResidueCode attribute) HF (cosmolkit.Element attribute) HG (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) HIC (cosmolkit.ResidueCode attribute) Hierarchy (cosmolkit.ChemCompModelErrorKind attribute) HIS (cosmolkit.ResidueCode attribute) HO (cosmolkit.Element attribute) HOH (cosmolkit.ResidueCode attribute) (cosmolkit.ResidueInfoKind attribute) HostUnreachable (cosmolkit.IoErrorKind attribute) HS (cosmolkit.Element attribute) HTG (cosmolkit.ResidueCode attribute) HTO (cosmolkit.ResidueCode attribute) Hybridization (class in cosmolkit) hybridization (cosmolkit.Atom attribute) Hybridization (cosmolkit.AtropisomerErrorKind attribute) hybridization (cosmolkit.BoundsQueryError property) Hybridization (cosmolkit.BoundsQueryErrorKind attribute) hybridization (cosmolkit.GenerationError property) Hybridization (cosmolkit.GenerationErrorKind attribute) hybridization (cosmolkit.MoleculeAtom attribute) Hybridization (cosmolkit.SanitizeErrorKind attribute) HybridizationAssignmentLength (cosmolkit.AtropisomerErrorKind attribute) HybridizationError HybridizationErrorKind (class in cosmolkit) HybridizationMatch (cosmolkit.AtomQueryPredicateKind attribute) Hydrog (cosmolkit.BioConnectionKind attribute) HYDROGEN (cosmolkit.BondOrder attribute) Hydrogen (cosmolkit.BondOrder attribute) (cosmolkit.DrawingErrorKind attribute) (cosmolkit.MolProcessingErrorKind attribute) hydrogen (cosmolkit.OperationError property) Hydrogen (cosmolkit.OperationErrorKind attribute) (cosmolkit.SmilesErrorKind attribute) HYDROGEN_BONDS (cosmolkit.CxSmilesFields attribute) hydrogen_contribution (cosmolkit.LabuteAsaContributions attribute) hydrogen_count (cosmolkit.ResidueInfo attribute) (cosmolkit.StereoError property) HydrogenAppend (cosmolkit.DrawingErrorKind attribute) HydrogenCount (cosmolkit.AtomQueryPredicateKind attribute) (cosmolkit.StereoErrorKind attribute) HydrogenCountOutOfRange (cosmolkit.TautomerRunErrorKind attribute) HydrogenCountOverflow (cosmolkit.ValenceErrorKind attribute) HydrogenError HydrogenErrorKind (class in cosmolkit) Hydrogens (cosmolkit.BioMoleculeConversionErrorKind attribute) (cosmolkit.DescriptorErrorKind attribute) hydrogens (cosmolkit.EnumerationError property) Hydrogens (cosmolkit.EnumerationErrorKind attribute) hydrogens (cosmolkit.GenerationError property) Hydrogens (cosmolkit.GenerationErrorKind attribute) hydrogens (cosmolkit.PruningError property) Hydrogens (cosmolkit.PruningErrorKind attribute) HYP (cosmolkit.ResidueCode attribute) I I (cosmolkit.Element attribute) (cosmolkit.ForceFieldIndexArgument attribute) (cosmolkit.ResidueCode attribute) i (cosmolkit.UffBuilderError property) IAS (cosmolkit.ResidueCode attribute) ICI (cosmolkit.ResidueCode attribute) ICT (cosmolkit.ResidueCode attribute) id (cosmolkit.AlignmentError property) (cosmolkit.Atom attribute) (cosmolkit.BioAtom attribute) (cosmolkit.BioChain attribute) (cosmolkit.BioDiffractionInfo attribute) (cosmolkit.BioExperimentalCrystalInfo attribute) (cosmolkit.BioModel attribute) (cosmolkit.BioNcsOperator attribute) (cosmolkit.BioRefinementInfo attribute) (cosmolkit.BioResidue attribute) (cosmolkit.BioTlsGroup attribute) (cosmolkit.Bond attribute) (cosmolkit.Conformer2D attribute) (cosmolkit.Conformer3D attribute) (cosmolkit.CoordinateValidationError property) (cosmolkit.CxCoordinateSelection attribute) (cosmolkit.FragmentCoordinateViewError property) (cosmolkit.MmcifTlsInfoError property) (cosmolkit.MolCoordinateSelection attribute) (cosmolkit.MoleculeAtom attribute) (cosmolkit.MolWriteError property) (cosmolkit.PdbModelTransitionError property) (cosmolkit.PdbWriteError property) (cosmolkit.ProteinAtomRef attribute) (cosmolkit.ProteinChainRef attribute) (cosmolkit.ProteinResidueRef attribute) (cosmolkit.QueryAtom attribute) (cosmolkit.QueryGraphError property) (cosmolkit.ReactionCoordinateSelection attribute) (cosmolkit.SmilesStereoError property) (cosmolkit.StereoError property) (cosmolkit.StereoGroup attribute) (cosmolkit.SubstanceGroup attribute) (cosmolkit.TopologyValidationError property) (cosmolkit.XyzWriteError property) id_code (cosmolkit.BioEntityDbRef attribute) IdentityField (cosmolkit.MmcifAtomSiteGroupingErrorKind attribute) IDO (cosmolkit.ResidueCode attribute) idx2 (cosmolkit.UffTypingError property) idx3 (cosmolkit.UffTypingError property) Ignore (cosmolkit.CoordinateZPolicy attribute) ignore_atom_map_numbers (cosmolkit.SmilesWriteParams attribute) ignore_atoms (cosmolkit.AtomPairFingerprintParams attribute) (cosmolkit.LegacyTopologicalTorsionParams attribute) (cosmolkit.MorganCallParams attribute) (cosmolkit.MorganFingerprintParams attribute) (cosmolkit.TopologicalFingerprintParams attribute) (cosmolkit.TopologicalTorsionCallParams attribute) (cosmolkit.TopologicalTorsionFingerprintParams attribute) ignore_hydrogens (cosmolkit.AllConformerRmsdParameters attribute) (cosmolkit.BestAlignmentParameters attribute) ignore_interfragment_interactions (cosmolkit.MmffConformerOptimizationParams attribute) (cosmolkit.MmffEvaluationParams attribute) (cosmolkit.MmffForceFieldParams attribute) (cosmolkit.MmffOptimizationParams attribute) (cosmolkit.UffConformerOptimizationParams attribute) (cosmolkit.UffEvaluationParams attribute) (cosmolkit.UffForceFieldParams attribute) (cosmolkit.UffOptimizationParams attribute) ignore_smoothing_failures (cosmolkit.EmbedParams attribute) ignore_ter (cosmolkit.BioPdbReadParams attribute) IgnoredAtomMaskLength (cosmolkit.PathErrorKind attribute) ILE (cosmolkit.ResidueCode attribute) IllegalCodepoint (cosmolkit.JsonErrorKind attribute) impl_fn (cosmolkit.MoleculeOpSpec attribute) implementation (cosmolkit.GenerationError property) implicit (cosmolkit.ValenceError property) Implicit (cosmolkit.ValencePhase attribute) implicit_hydrogens (cosmolkit.AtomMetadata attribute) (cosmolkit.MoleculeAtom attribute) implicit_len (cosmolkit.CanonicalRankError property) (cosmolkit.FragmentWriteInputError property) implicit_properties (cosmolkit.Reaction attribute) ImplicitHydrogen (cosmolkit.LigandRef attribute) (cosmolkit.UffPreparedValenceField attribute) ImplicitHydrogenCount (cosmolkit.AtomQueryPredicateKind attribute) (cosmolkit.AtomRangeDataFunctionKind attribute) ImplicitHydrogenCountLessEqual (cosmolkit.AtomQueryPredicateKind attribute) ImplicitReplacementNotInSource (cosmolkit.StereoOrderErrorKind attribute) ImplicitReplacementOutOfRange (cosmolkit.StereoOrderErrorKind attribute) ImplicitReplacementRetained (cosmolkit.StereoOrderErrorKind attribute) ImplicitValence (cosmolkit.AtomQueryPredicateKind attribute) ImplicitValenceCacheNotInitialized (cosmolkit.ValenceErrorKind attribute) ImpossibleCrystalAngle (cosmolkit.BioStructureErrorKind attribute) IN (cosmolkit.Element attribute) inchi (cosmolkit.InchiResult attribute) inchi_to_key() (in module cosmolkit) InchiDiagnostic (class in cosmolkit) InchiDiagnosticLevel (class in cosmolkit) InchiError InchiErrorKind (class in cosmolkit) InchiReadParams (class in cosmolkit) InchiResult (class in cosmolkit) InchiWriteParams (class in cosmolkit) incident_count (cosmolkit.ParserStereoOrderError property) include_atom_maps (cosmolkit.SmartsWriteParams attribute) include_chirality (cosmolkit.AtomPairAtomInvariantsGenerator attribute) (cosmolkit.AtomPairFingerprintParams attribute) (cosmolkit.AtomPairGeneratorParams attribute) (cosmolkit.LegacyTopologicalTorsionParams attribute) (cosmolkit.MorganBondInvariantsGenerator attribute) (cosmolkit.MorganFingerprintParams attribute) (cosmolkit.MorganGeneratorParams attribute) (cosmolkit.MorganSettings attribute) (cosmolkit.TopologicalTorsionFingerprintParams attribute) (cosmolkit.TopologicalTorsionGeneratorParams attribute) (cosmolkit.TopologicalTorsionSettings attribute) include_coordinates (cosmolkit.MolBlockWriteParams attribute) include_cx (cosmolkit.ReactionWriteParams attribute) include_dative_bonds (cosmolkit.ReactionWriteParams attribute) (cosmolkit.RingSearchParams attribute) (cosmolkit.SmartsWriteParams attribute) (cosmolkit.SmilesWriteParams attribute) include_hydrogen_bonds (cosmolkit.RingSearchParams attribute) include_redundant_environments (cosmolkit.MorganFingerprintParams attribute) (cosmolkit.MorganGeneratorParams attribute) (cosmolkit.MorganSettings attribute) include_ring_membership (cosmolkit.MorganFingerprintParams attribute) (cosmolkit.MorganGeneratorParams attribute) include_stereo (cosmolkit.MolBlockWriteParams attribute) include_sulfur_phosphorus (cosmolkit.DescriptorError property) Inclusive (cosmolkit.AtomRangeBoundsKind attribute) IncompleteCommit (cosmolkit.OperationErrorKind attribute) IncompleteCoverage (cosmolkit.BioStructureErrorKind attribute) IncompleteParameterLine (cosmolkit.CrystalffTorsionPreferencesErrorKind attribute) IncompleteSourceBatchMasks (cosmolkit.TopologyEditErrorKind attribute) InconsistentInsertionCode (cosmolkit.MmcifSequenceIdErrorKind attribute) IncorrectNumberOfStereoAtoms (cosmolkit.CipLabelerErrorKind attribute) index (cosmolkit.AlignmentError property) (cosmolkit.BatchError property) (cosmolkit.BioStructureError property) (cosmolkit.BoundsMatrixError property) (cosmolkit.CipLabelerError property) (cosmolkit.Coordinate2DTemplateError property) (cosmolkit.CxQueryLoweringError property) (cosmolkit.DistGeomForceFieldError attribute) (cosmolkit.DrawingError property) (cosmolkit.EmbedFailureCountError property) (cosmolkit.EmbedSeedError property) (cosmolkit.FingerprintBatchError property) (cosmolkit.FingerprintError property) (cosmolkit.ForceFieldKernelError property) (cosmolkit.MmcifAtomSiteGroupingError property) (cosmolkit.PotentialStereoCenter attribute) (cosmolkit.ProteinProjectionError property) (cosmolkit.ReactionModelError property) (cosmolkit.ReactionProductError property) (cosmolkit.ReactionRunError property) (cosmolkit.SdfReadError property) (cosmolkit.SdfRecord attribute) (cosmolkit.SdfRecordMetadata attribute) (cosmolkit.SmartsWriteError property) (cosmolkit.SmilesParseError property) (cosmolkit.SubstanceGroupId attribute) (cosmolkit.SubstructMatchError property) (cosmolkit.TautomerCatalogError property) (cosmolkit.TopologicalTorsionPathScoreError property) (cosmolkit.UffInversionContributionError property) (cosmolkit.UffTypingError property) (cosmolkit.WedgeError property) IndexOutOfBounds (cosmolkit.BoundsMatrixErrorKind attribute) IndexOutOfRange (cosmolkit.ForceFieldKernelErrorKind attribute) (cosmolkit.UffInversionContributionErrorKind attribute) IndexOverflow (cosmolkit.DistGeomForceFieldErrorKind attribute) info (cosmolkit.BioSelectionParseError property) (cosmolkit.BioStructureSourceState attribute) (cosmolkit.ProteinResidueRef attribute) (cosmolkit.ResidueIdentity attribute) info_string() (cosmolkit.AtomPairAtomInvariantsGenerator method) (cosmolkit.AtomPairGeneratorParams method) (cosmolkit.MorganFingerprintGenerator method) (cosmolkit.MorganGeneratorParams method) (cosmolkit.TopologicalTorsionFingerprintGenerator method) (cosmolkit.TopologicalTorsionGeneratorParams method) initial_seed (cosmolkit.McsParameters attribute) InitialCoords (cosmolkit.EmbedFailureCause attribute) Initialization (cosmolkit.MolecularForceFieldErrorKind attribute) initialization (cosmolkit.ReactionApplyError property) Initialization (cosmolkit.ReactionApplyErrorKind attribute) initialization (cosmolkit.ReactionRunError property) Initialization (cosmolkit.ReactionRunErrorKind attribute) Initialize (cosmolkit.OptimizationStageErrorKind attribute) initialized (cosmolkit.RecursiveStructureQuery attribute) InitialSeedBondMissing (cosmolkit.McsErrorKind attribute) InitialSeedMatch (cosmolkit.McsErrorKind attribute) InitialSeedParse (cosmolkit.McsErrorKind attribute) Input (cosmolkit.AvalonFingerprintErrorKind attribute) (cosmolkit.ConformerOptimizerCauseKind attribute) (cosmolkit.GenerationErrorKind attribute) (cosmolkit.GraphBoundsErrorKind attribute) input (cosmolkit.OperationError property) Input (cosmolkit.PruningErrorKind attribute) input (cosmolkit.ResidueCodeParseError property) (cosmolkit.UffTypingError property) input_atoms (cosmolkit.AromaticityError property) input_bonds (cosmolkit.AromaticityError property) input_count (cosmolkit.OperationError property) input_format (cosmolkit.BioStructure attribute) (cosmolkit.BioStructureParts attribute) (cosmolkit.PdbReaderCause property) (cosmolkit.Protein attribute) input_index (cosmolkit.SerialConformerOptimizationError property) InputFormat (cosmolkit.PdbReaderCauseKind attribute) InRing (cosmolkit.AtomQueryPredicateKind attribute) InRingOfSize (cosmolkit.AtomQueryPredicateKind attribute) (cosmolkit.BondQueryPredicateKind attribute) InRingOfSizeGreaterEqual (cosmolkit.AtomQueryPredicateKind attribute) InRingOfSizeLessEqual (cosmolkit.AtomQueryPredicateKind attribute) ins_code (cosmolkit.PdbSeqId attribute) insertion_code (cosmolkit.ResidueAddress attribute) Int (cosmolkit.PropertyValueKind attribute) Int() (cosmolkit.PropertyValue static method) integer_property (cosmolkit.SdfWriteError property) IntegerOutsideSourceDefinedRange (cosmolkit.PdbHelixErrorKind attribute) (cosmolkit.PdbRemark200ErrorKind attribute) (cosmolkit.PdbRemark350ErrorKind attribute) (cosmolkit.PdbRemark3ErrorKind attribute) (cosmolkit.PdbRemarkFinalizationErrorKind attribute) (cosmolkit.PdbRemarkMetadataErrorKind attribute) (cosmolkit.PdbSheetErrorKind attribute) IntegerOverflow (cosmolkit.AromaticityErrorKind attribute) (cosmolkit.ConjugationErrorKind attribute) (cosmolkit.HybridizationErrorKind attribute) (cosmolkit.KekulizeErrorKind attribute) IntegerProperty (cosmolkit.SdfWriteErrorKind attribute) Interrupted (cosmolkit.EmbedTermination attribute) (cosmolkit.IoErrorKind attribute) into_bio_structure() (cosmolkit.Protein method) into_parts() (cosmolkit.BioStructure method) IntVector (cosmolkit.PropertyValueKind attribute) IntVector() (cosmolkit.PropertyValue static method) invalid (cosmolkit.FingerprintJsonError property) Invalid (cosmolkit.FingerprintJsonErrorKind attribute) (cosmolkit.ReactionInitializationErrorKind attribute) invalid_bond (cosmolkit.TopologyEditError property) invalid_coordinates (cosmolkit.OperationError property) invalid_count (cosmolkit.MoleculeBatch attribute) invalid_mapping (cosmolkit.TopologyEditError property) invalid_mask (cosmolkit.MoleculeBatch attribute) invalid_property (cosmolkit.OperationError property) invalid_query (cosmolkit.MatchError property) invalid_result (cosmolkit.TopologyEditError property) invalid_source (cosmolkit.TopologyEditError property) invalid_target (cosmolkit.MatchError property) invalid_topology (cosmolkit.OperationError property) invalid_topology_edit (cosmolkit.OperationError property) InvalidAdditionPlan (cosmolkit.HydrogenErrorKind attribute) InvalidAlgorithmResult (cosmolkit.OperationErrorKind attribute) InvalidAngle (cosmolkit.Coordinate2DLayoutErrorKind attribute) InvalidArchive (cosmolkit.PickleErrorKind attribute) InvalidArgument (cosmolkit.BondEndPointsParseErrorKind attribute) InvalidArguments (cosmolkit.AvalonEngineErrorKind attribute) (cosmolkit.FingerprintErrorKind attribute) (cosmolkit.LayeredFingerprintErrorKind attribute) (cosmolkit.PatternFingerprintErrorKind attribute) (cosmolkit.TopologicalFingerprintErrorKind attribute) InvalidArrayElement (cosmolkit.MmjsonValueErrorKind attribute) InvalidAtomDegree (cosmolkit.PotentialStereoErrorKind attribute) InvalidAtomDescriptor (cosmolkit.CipLabelerErrorKind attribute) InvalidAtomIndex (cosmolkit.MolecularForceFieldErrorKind attribute) InvalidAtomPrimitive (cosmolkit.SmartsParseErrorKind attribute) InvalidAtropisomerStereo (cosmolkit.AtropisomerErrorKind attribute) InvalidAttributeValue (cosmolkit.XmlParseErrorKind attribute) InvalidBond (cosmolkit.TopologyEditErrorKind attribute) InvalidBondDegree (cosmolkit.PotentialStereoErrorKind attribute) InvalidBondDescriptor (cosmolkit.CipLabelerErrorKind attribute) InvalidBondEndpoint (cosmolkit.QueryGraphErrorKind attribute) InvalidBondOrder (cosmolkit.UffBondMathErrorKind attribute) InvalidBound (cosmolkit.BoundsMatrixErrorKind attribute) InvalidBounds (cosmolkit.GraphBoundsErrorKind attribute) InvalidCategory (cosmolkit.MmjsonStructureErrorKind attribute) InvalidCause (cosmolkit.EmbedFailureCountErrorKind attribute) InvalidChar (cosmolkit.XmlParseErrorKind attribute) InvalidChar2 (cosmolkit.XmlParseErrorKind attribute) InvalidCharacterData (cosmolkit.XmlParseErrorKind attribute) InvalidChiralPermutation (cosmolkit.PotentialStereoErrorKind attribute) InvalidComment (cosmolkit.XmlParseErrorKind attribute) InvalidConformer (cosmolkit.DoubleBondStereoErrorKind attribute) InvalidConformerId (cosmolkit.MmffBuilderErrorKind attribute) InvalidConnectivityPath (cosmolkit.DescriptorErrorKind attribute) InvalidConstraintBounds (cosmolkit.MolecularForceFieldErrorKind attribute) InvalidConstraintRange (cosmolkit.MolecularForceFieldErrorKind attribute) InvalidCoordinates (cosmolkit.AlignmentErrorKind attribute) (cosmolkit.AtropisomerErrorKind attribute) (cosmolkit.CoordinateInputErrorKind attribute) (cosmolkit.HydrogenErrorKind attribute) (cosmolkit.MatrixErrorKind attribute) (cosmolkit.OperationErrorKind attribute) (cosmolkit.TransformErrorKind attribute) InvalidCpuList (cosmolkit.ThreadCountErrorKind attribute) InvalidCrippenOptionalRows (cosmolkit.DescriptorErrorKind attribute) InvalidData (cosmolkit.IoErrorKind attribute) InvalidDefaultRow (cosmolkit.Coordinate2DTemplateErrorKind attribute) InvalidDerivedCache (cosmolkit.OperationErrorKind attribute) InvalidDimensions (cosmolkit.DrawingErrorKind attribute) InvalidDirection (cosmolkit.DoubleBondStereoErrorKind attribute) InvalidElementNamePrefix (cosmolkit.XmlParseErrorKind attribute) InvalidEmbedParametersJson (cosmolkit.ConformerErrorKind attribute) InvalidEndpointDegree (cosmolkit.DoubleBondStereoErrorKind attribute) InvalidEnumValue (cosmolkit.PickleErrorKind attribute) InvalidEquivalentLevel (cosmolkit.MmffTorLookupErrorKind attribute) InvalidExperimentalTorsionVersion (cosmolkit.CrystalffTorsionPreferencesErrorKind attribute) InvalidExplicitValenceInput (cosmolkit.ValenceErrorKind attribute) InvalidExternalID (cosmolkit.XmlParseErrorKind attribute) InvalidFilename (cosmolkit.IoErrorKind attribute) InvalidFixedAtom (cosmolkit.MolecularForceFieldErrorKind attribute) InvalidFlipperAtom (cosmolkit.EnumerationErrorKind attribute) InvalidFlipperBond (cosmolkit.EnumerationErrorKind attribute) InvalidFloat (cosmolkit.MmffParamParseCauseKind attribute) InvalidFloatToken (cosmolkit.CrystalffTorsionPreferencesErrorKind attribute) InvalidFoldFactor (cosmolkit.FingerprintErrorKind attribute) InvalidFormat (cosmolkit.BatchImageErrorKind attribute) InvalidGraph (cosmolkit.CxQueryLoweringErrorKind attribute) (cosmolkit.QueryCompileErrorKind attribute) (cosmolkit.SmartsWriteErrorKind attribute) InvalidHallKierContributionRows (cosmolkit.DescriptorErrorKind attribute) InvalidInput (cosmolkit.InchiErrorKind attribute) (cosmolkit.IoErrorKind attribute) InvalidInsertionCode (cosmolkit.MmcifSequenceIdErrorKind attribute) InvalidIntegerToken (cosmolkit.CrystalffTorsionPreferencesErrorKind attribute) InvalidInternalState (cosmolkit.CipLabelerErrorKind attribute) InvalidKind (cosmolkit.PropertyIntReadErrorKind attribute) (cosmolkit.PropertyUIntReadErrorKind attribute) (cosmolkit.PropertyULongReadErrorKind attribute) InvalidLengthRange (cosmolkit.PathErrorKind attribute) InvalidLoop (cosmolkit.CifReadErrorKind attribute) InvalidMapping (cosmolkit.HydrogenErrorKind attribute) (cosmolkit.StereoOrderErrorKind attribute) (cosmolkit.TopologyEditErrorKind attribute) InvalidMolecule (cosmolkit.PickleErrorKind attribute) InvalidName (cosmolkit.XmlParseErrorKind attribute) InvalidNeighborOrder (cosmolkit.CipDescriptorErrorKind attribute) InvalidNumber (cosmolkit.JsonErrorKind attribute) InvalidOperations (cosmolkit.SanitizeErrorKind attribute) InvalidParameterization (cosmolkit.MolecularForceFieldErrorKind attribute) InvalidParameterSourceFormat (cosmolkit.CrystalffTorsionPreferencesErrorKind attribute) InvalidProperty (cosmolkit.HydrogenErrorKind attribute) (cosmolkit.OperationErrorKind attribute) InvalidPropertyKind (cosmolkit.CanonicalRankErrorKind attribute) (cosmolkit.CipLabelerErrorKind attribute) (cosmolkit.DoubleBondStereoErrorKind attribute) (cosmolkit.MolPostErrorKind attribute) (cosmolkit.PotentialStereoErrorKind attribute) (cosmolkit.SmartsWriteErrorKind attribute) InvalidPropertyList (cosmolkit.HydrogenErrorKind attribute) (cosmolkit.OperationErrorKind attribute) InvalidQuery (cosmolkit.MatchErrorKind attribute) InvalidQueryState (cosmolkit.AromaticityErrorKind attribute) (cosmolkit.CipRankErrorKind attribute) (cosmolkit.HydrogenErrorKind attribute) (cosmolkit.KekulizeErrorKind attribute) (cosmolkit.SanitizeErrorKind attribute) InvalidRandomSeed (cosmolkit.EmbedSeedErrorKind attribute) InvalidRankProperty (cosmolkit.Coordinate2DLayoutErrorKind attribute) InvalidReconstructionOrigin (cosmolkit.OperationErrorKind attribute) InvalidRemovalCandidate (cosmolkit.HydrogenErrorKind attribute) InvalidResult (cosmolkit.TopologyEditErrorKind attribute) InvalidRingInfo (cosmolkit.PotentialStereoErrorKind attribute) InvalidRingStereoReference (cosmolkit.PotentialStereoErrorKind attribute) InvalidSequenceNumber (cosmolkit.MmcifSequenceIdErrorKind attribute) InvalidShortestPathDag (cosmolkit.RingDecomposerErrorKind attribute) InvalidSize (cosmolkit.SvgParseErrorKind attribute) InvalidSource (cosmolkit.TopologyEditErrorKind attribute) InvalidSourceOutput (cosmolkit.InchiErrorKind attribute) InvalidSpan (cosmolkit.MmjsonValueErrorKind attribute) InvalidState (cosmolkit.BondDirectionStereoErrorKind attribute) (cosmolkit.PdbPostprocessErrorKind attribute) InvalidStereoDescriptor (cosmolkit.CipLabelerErrorKind attribute) InvalidStereoRank (cosmolkit.WedgeErrorKind attribute) InvalidStereoRankType (cosmolkit.WedgeErrorKind attribute) InvalidStereoReferences (cosmolkit.PotentialStereoErrorKind attribute) InvalidStereoTransition (cosmolkit.HydrogenErrorKind attribute) InvalidStoredDescriptor (cosmolkit.CipDescriptorErrorKind attribute) InvalidString (cosmolkit.XmlParseErrorKind attribute) InvalidStructure (cosmolkit.BioPdbWriteErrorKind attribute) InvalidSubsetTopology (cosmolkit.PathErrorKind attribute) InvalidTarget (cosmolkit.MatchErrorKind attribute) InvalidTargetValue (cosmolkit.TransformErrorKind attribute) InvalidText (cosmolkit.BioMmcifWriteErrorKind attribute) InvalidTolerance (cosmolkit.MolecularForceFieldErrorKind attribute) InvalidTopology (cosmolkit.AdjustHsErrorKind attribute) (cosmolkit.AromaticityErrorKind attribute) (cosmolkit.AtropisomerErrorKind attribute) (cosmolkit.CipLabelerErrorKind attribute) (cosmolkit.CipRankErrorKind attribute) (cosmolkit.CleanupErrorKind attribute) (cosmolkit.ConjugationErrorKind attribute) (cosmolkit.Coordinate2DErrorKind attribute) (cosmolkit.Coordinate2DTemplateErrorKind attribute) (cosmolkit.DescriptorErrorKind attribute) (cosmolkit.DoubleBondStereoErrorKind attribute) (cosmolkit.FragmentWriteInputErrorKind attribute) (cosmolkit.HybridizationErrorKind attribute) (cosmolkit.HydrogenErrorKind attribute) (cosmolkit.KekulizeErrorKind attribute) (cosmolkit.LegacyStereoErrorKind attribute) (cosmolkit.MatrixErrorKind attribute) (cosmolkit.MoleculeHashErrorKind attribute) (cosmolkit.OperationErrorKind attribute) (cosmolkit.PathErrorKind attribute) (cosmolkit.PotentialStereoErrorKind attribute) (cosmolkit.QueryMatchContextErrorKind attribute) (cosmolkit.RadicalErrorKind attribute) (cosmolkit.RingFindingErrorKind attribute) (cosmolkit.SanitizeErrorKind attribute) (cosmolkit.StereoErrorKind attribute) (cosmolkit.StereoOrderErrorKind attribute) (cosmolkit.StereoReadErrorKind attribute) (cosmolkit.TopologicalTorsionPathScoreErrorKind attribute) (cosmolkit.TransformErrorKind attribute) (cosmolkit.ValenceErrorKind attribute) InvalidTopologyEdit (cosmolkit.OperationErrorKind attribute) InvalidTopologyMapping (cosmolkit.OperationErrorKind attribute) InvalidUnicodeEscape (cosmolkit.JsonErrorKind attribute) InvalidUnsigned (cosmolkit.MmffParamParseCauseKind attribute) InvalidUtf16TrailSurrogate (cosmolkit.JsonErrorKind attribute) InvalidUtf8 (cosmolkit.JsonErrorKind attribute) (cosmolkit.MmjsonValueErrorKind attribute) (cosmolkit.TautomerCatalogErrorKind attribute) InvalidValence (cosmolkit.PotentialStereoErrorKind attribute) (cosmolkit.StereoErrorKind attribute) (cosmolkit.ValenceErrorKind attribute) InvalidValenceRow (cosmolkit.AdjustHsErrorKind attribute) (cosmolkit.AromaticityErrorKind attribute) (cosmolkit.ConjugationErrorKind attribute) (cosmolkit.HybridizationErrorKind attribute) InvalidValenceRows (cosmolkit.DescriptorErrorKind attribute) InvalidValenceValue (cosmolkit.PotentialStereoErrorKind attribute) (cosmolkit.StereoErrorKind attribute) InvalidValue (cosmolkit.CifReadErrorKind attribute) InvalidWeightSum (cosmolkit.TransformErrorKind attribute) InvalidXmlPrefixUri (cosmolkit.XmlParseErrorKind attribute) Invariant (cosmolkit.ReactionProductErrorKind attribute) invariant (cosmolkit.SubstructMatchError property) InvariantCount (cosmolkit.CipRankErrorKind attribute) InvariantOutOfRange (cosmolkit.CipRankErrorKind attribute) invariants (cosmolkit.MorganFingerprintParams attribute) InverseMismatch (cosmolkit.MappingValidationErrorKind attribute) inversion (cosmolkit.DistGeomForceFieldError attribute) Inversion (cosmolkit.DistGeomForceFieldErrorKind attribute) InversionContribution (cosmolkit.UffBuilderErrorKind attribute) Io (cosmolkit.BioMmcifWriteErrorKind attribute) (cosmolkit.BioPdbWriteErrorKind attribute) (cosmolkit.BioReadErrorKind attribute) (cosmolkit.DrawingWriteErrorKind attribute) (cosmolkit.MolecularIoErrorKind attribute) (cosmolkit.SerdeJsonCategory attribute) io_error_kind (cosmolkit.SerdeJsonError property) io_roundtrip (cosmolkit.MoleculeOpSpec attribute) IOD (cosmolkit.ResidueCode attribute) IoError IoErrorKind (class in cosmolkit) IOH (cosmolkit.ResidueCode attribute) IONIC (cosmolkit.BondOrder attribute) Ionic (cosmolkit.BondOrder attribute) IPA (cosmolkit.ResidueCode attribute) IPH (cosmolkit.ResidueCode attribute) IR (cosmolkit.Element attribute) is_2d (cosmolkit.ReactionCoordinateSelection attribute) is_3d (cosmolkit.Conformer3D attribute) (cosmolkit.Coordinate3DInputParams attribute) (cosmolkit.ReactionCoordinateSelection attribute) is_amino_acid (cosmolkit.ResidueInfo attribute) is_aromatic (cosmolkit.Atom attribute) (cosmolkit.Bond attribute) (cosmolkit.MoleculeAtom attribute) (cosmolkit.QueryAtom attribute) is_auto (cosmolkit.ReactionCoordinateSelection attribute) is_crystal (cosmolkit.BioCrystalInfo attribute) is_data (cosmolkit.SerdeJsonError property) is_dna (cosmolkit.ResidueInfo attribute) is_empty (cosmolkit.BioCoordinateBlock attribute) (cosmolkit.BioRowSpan attribute) (cosmolkit.MoleculeBatch attribute) (cosmolkit.PdbReadFlags attribute) (cosmolkit.PdbWriteFlags attribute) (cosmolkit.SanitizeOperations attribute) (cosmolkit.SdfDataset attribute) (cosmolkit.TautomerEnumeration attribute) (cosmolkit.TautomerProgress attribute) is_end (cosmolkit.SdfRecordStream attribute) is_eof (cosmolkit.SerdeJsonError property) is_initialized (cosmolkit.Reaction attribute) is_io (cosmolkit.SerdeJsonError property) is_modified_amino_acid (cosmolkit.ResidueInfo attribute) is_prop_computed() (cosmolkit.MoleculeProperties method) is_query (cosmolkit.AvalonFingerprintParams attribute) is_rna (cosmolkit.ResidueInfo attribute) is_standard (cosmolkit.ProteinResidueRef attribute) is_syntax (cosmolkit.SerdeJsonError property) is_tabulated (cosmolkit.ResidueIdentity attribute) is_valid (cosmolkit.MmffProperties attribute) (cosmolkit.ReactionValidationReport attribute) is_water (cosmolkit.ResidueInfo attribute) IsADirectory (cosmolkit.IoErrorKind attribute) IsAromatic (cosmolkit.AtomQueryPredicateKind attribute) (cosmolkit.BondQueryPredicateKind attribute) IsBridgehead (cosmolkit.AtomQueryPredicateKind attribute) IsConjugated (cosmolkit.BondQueryPredicateKind attribute) IsInRing (cosmolkit.BondQueryPredicateKind attribute) isoform (cosmolkit.BioEntityDbRef attribute) isomeric_smiles (cosmolkit.RandomSmilesWriteParams attribute) (cosmolkit.ReactionWriteParams attribute) (cosmolkit.SmartsWriteParams attribute) (cosmolkit.SmilesWriteParams attribute) isotope (cosmolkit.Atom attribute) Isotope (cosmolkit.AtomQueryPredicateKind attribute) isotope (cosmolkit.MoleculeAtom attribute) (cosmolkit.PeriodicTableError property) (cosmolkit.QueryAtom attribute) isotope_mass_number (cosmolkit.BioAtom attribute) (cosmolkit.BioAtomRow attribute) Isotopes (cosmolkit.McsAtomComparator attribute) issue (cosmolkit.OperationError property) IsUnsaturated (cosmolkit.AtomQueryPredicateKind attribute) iter() (cosmolkit.SdfDataset method) (cosmolkit.TautomerEnumeration method) iterations (cosmolkit.ForceFieldMinimizeOutcome attribute) (cosmolkit.PotentialStereoError property) J J (cosmolkit.ForceFieldIndexArgument attribute) j (cosmolkit.UffBuilderError property) JEF (cosmolkit.ResidueCode attribute) Json (cosmolkit.MorganErrorKind attribute) (cosmolkit.TopologicalTorsionErrorKind attribute) JsonError JsonErrorKind (class in cosmolkit) K K (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) kappa_1() (cosmolkit.Molecule method) kappa_2() (cosmolkit.Molecule method) kappa_3() (cosmolkit.Molecule method) KCX (cosmolkit.ResidueCode attribute) kdg() (cosmolkit.EmbedParams static method) KEEP (cosmolkit.BatchErrorMode attribute) KEEP_ALTERNATE_AND_PSEUDO_ATOMS (cosmolkit.PdbReadFlags attribute) KeepErrors (cosmolkit.BatchErrorMode attribute) kekule (cosmolkit.RandomSmilesWriteParams attribute) (cosmolkit.SmilesWriteParams attribute) kekulize (cosmolkit.AromaticityError property) Kekulize (cosmolkit.AromaticityErrorKind attribute) kekulize (cosmolkit.ChemistryProblemError property) Kekulize (cosmolkit.ChemistryProblemErrorKind attribute) kekulize (cosmolkit.CipLabelerError property) Kekulize (cosmolkit.CipLabelerErrorKind attribute) (cosmolkit.DrawingErrorKind attribute) kekulize (cosmolkit.MmffMolPropertiesError property) Kekulize (cosmolkit.MmffMolPropertiesErrorKind attribute) kekulize (cosmolkit.MolBlockWriteParams attribute) (cosmolkit.MolWriteError property) Kekulize (cosmolkit.MolWriteErrorKind attribute) kekulize (cosmolkit.OperationError property) Kekulize (cosmolkit.OperationErrorKind attribute) (cosmolkit.PdbWriteErrorKind attribute) (cosmolkit.SanitizeErrorKind attribute) KEKULIZE (cosmolkit.SanitizeOperations attribute) Kekulize (cosmolkit.SanitizeStage attribute) kekulize (cosmolkit.TautomerRunError property) Kekulize (cosmolkit.TautomerRunErrorKind attribute) kekulize_bonds_() (cosmolkit.Molecule method) kekulize_bonds_with_params_() (cosmolkit.Molecule method) KekulizeError KekulizeErrorKind (class in cosmolkit) KekulizeParams (class in cosmolkit) kernel (cosmolkit.DistGeomForceFieldError attribute) Kernel (cosmolkit.DistGeomForceFieldErrorKind attribute) kernel (cosmolkit.MmffOptimizationFailure property) Kernel (cosmolkit.MmffOptimizationFailureKind attribute) (cosmolkit.MolecularForceFieldErrorKind attribute) kernel (cosmolkit.UffEvaluationFailure attribute) Kernel (cosmolkit.UffEvaluationFailureKind attribute) KernelCoordinateRowCount (cosmolkit.FragmentCoordinateViewErrorKind attribute) KernelCoordinateRowWidth (cosmolkit.FragmentCoordinateViewErrorKind attribute) KET (cosmolkit.ResidueInfoKind attribute) key (cosmolkit.Coordinate2DLayoutError property) (cosmolkit.MissingPropertyError property) (cosmolkit.OperationError property) (cosmolkit.ReactionProductError property) (cosmolkit.SmilesParseError property) kind (cosmolkit.BioChain attribute) (cosmolkit.BioChainRow attribute) (cosmolkit.BioConnection attribute) (cosmolkit.BioEntityRow attribute) (cosmolkit.BioResidue attribute) (cosmolkit.BioResidueRow attribute) (cosmolkit.BoundsMatrixError property) (cosmolkit.CanonicalRankError property) (cosmolkit.CifReadError property) (cosmolkit.CipLabelerError property) (cosmolkit.DoubleBondStereoError property) (cosmolkit.DoubleLexicalReadError property) (cosmolkit.ForceFieldError property) (cosmolkit.IoError property) (cosmolkit.JsonError property) (cosmolkit.McsError property) (cosmolkit.MmffForceFieldError property) (cosmolkit.MmjsonStructureError property) (cosmolkit.MolPostError property) (cosmolkit.PotentialStereoCenter attribute) (cosmolkit.PotentialStereoError property) (cosmolkit.PropertyIntReadError property) (cosmolkit.PropertyStringError property) (cosmolkit.PropertyUIntReadError property) (cosmolkit.PropertyULongReadError property) (cosmolkit.PropertyValue attribute) (cosmolkit.ProteinChainRef attribute) (cosmolkit.ProteinResidueRef attribute) (cosmolkit.ReactionProductError property) (cosmolkit.ReactionValidationIssue attribute) (cosmolkit.ResidueInfo attribute) (cosmolkit.ResidueSequenceError property) (cosmolkit.SdfReadError property) (cosmolkit.SmartsWriteError property) (cosmolkit.StereoGroup attribute) (cosmolkit.SubstanceGroup attribute) (cosmolkit.TopologyEditError property) (cosmolkit.UffForceFieldError property) (cosmolkit.UffOptimizationError property) (cosmolkit.UffParameterError property) (cosmolkit.WedgeError property) KPI (cosmolkit.ResidueCode attribute) KR (cosmolkit.Element attribute) KtermViolation (cosmolkit.EmbedFailureCause attribute) L l (cosmolkit.BioTlsGroup attribute) LA (cosmolkit.Element attribute) label (cosmolkit.TemplateAttachment attribute) (cosmolkit.TemplateAttachmentOrderError property) label_asym_id (cosmolkit.ChainSourceIds attribute) label_entity_id (cosmolkit.ResidueSourceIds attribute) label_seq_begin (cosmolkit.BioEntityDbRef attribute) label_seq_end (cosmolkit.BioEntityDbRef attribute) label_seq_id (cosmolkit.ResidueSourceIds attribute) LabelAddress (cosmolkit.MmcifConnectionErrorKind attribute) LabelSequenceId (cosmolkit.MmcifLabelAddressErrorKind attribute) LabelSequenceNumber (cosmolkit.MmcifAtomSiteGroupingErrorKind attribute) labute_asa() (cosmolkit.Molecule method) labute_asa_contributions() (cosmolkit.Molecule method) labute_asa_contributions_with_params() (cosmolkit.Molecule method) labute_asa_with_params() (cosmolkit.Molecule method) LabuteAsaContributions (class in cosmolkit) LAlpha (cosmolkit.BioHelixClass attribute) largest_fragment() (cosmolkit.Molecule method) LAT (cosmolkit.ResidueCode attribute) LaterCoordinateBlock (cosmolkit.CoordinateBlockSelectionErrorKind attribute) LayeredFingerprintError LayeredFingerprintErrorKind (class in cosmolkit) LayeredFingerprintLayers (class in cosmolkit) LayeredFingerprintParams (class in cosmolkit) LayeredFingerprintResult (class in cosmolkit) layers (cosmolkit.LayeredFingerprintParams attribute) LazyMultiple (cosmolkit.MoleculeOpOutput attribute) LBT (cosmolkit.ResidueCode attribute) LDA (cosmolkit.ResidueCode attribute) left (cosmolkit.FingerprintError property) (cosmolkit.PatternFingerprintError property) legacy_stereo (cosmolkit.TautomerRunError property) LegacyStereo (cosmolkit.MolProcessingErrorKind attribute) (cosmolkit.MorganErrorKind attribute) (cosmolkit.TautomerRunErrorKind attribute) LegacyStereoError LegacyStereoErrorKind (class in cosmolkit) LegacyTopologicalTorsionParams (class in cosmolkit) len (cosmolkit.BioCoordinateBlock attribute) (cosmolkit.BioRowSpan attribute) (cosmolkit.BioStructureError property) (cosmolkit.FingerprintBatch attribute) (cosmolkit.FragmentWriteInputError property) (cosmolkit.MoleculeBatch attribute) (cosmolkit.PdbAtomFieldError attribute) (cosmolkit.SdfDataset attribute) (cosmolkit.TautomerCatalogError property) (cosmolkit.TautomerEnumeration attribute) (cosmolkit.TautomerProgress attribute) length (cosmolkit.AtomPairError property) (cosmolkit.BioHelix attribute) (cosmolkit.BioPdbWriteError property) Length (cosmolkit.MappingValidationErrorKind attribute) length (cosmolkit.MmcifAtomSiteGroupingError property) (cosmolkit.PathError property) (cosmolkit.PickleError property) (cosmolkit.SparseCountFingerprint attribute) (cosmolkit.SparseCountFingerprint32 attribute) LengthOverflow (cosmolkit.PathErrorKind attribute) LessEqual (cosmolkit.AtomRangeBoundsKind attribute) letter (cosmolkit.ResidueSequenceError property) LEU (cosmolkit.ResidueCode attribute) level (cosmolkit.InchiDiagnostic attribute) (cosmolkit.MmffTorLookupError property) (cosmolkit.ReactionRunError property) Lexical (cosmolkit.PropertyIntReadErrorKind attribute) (cosmolkit.PropertyUIntReadErrorKind attribute) (cosmolkit.PropertyULongReadErrorKind attribute) LexicalOverflow (cosmolkit.PropertyULongReadErrorKind attribute) LGamma (cosmolkit.BioHelixClass attribute) LI (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) Ligand (cosmolkit.ResidueKind attribute) LigandOnly (cosmolkit.ChainKind attribute) LigandRef (class in cosmolkit) ligands (cosmolkit.TetrahedralStereo attribute) limit (cosmolkit.CipLabelerError property) (cosmolkit.PotentialStereoError property) line (cosmolkit.CifReadError property) (cosmolkit.Coordinate2DTemplateError property) (cosmolkit.CrystalffTorsionPreferencesError property) (cosmolkit.JsonError property) (cosmolkit.MmffParamParseError property) (cosmolkit.SdfReadError property) (cosmolkit.SerdeJsonError property) (cosmolkit.XyzReadError property) line_len (cosmolkit.PdbRemarkError property) line_number (cosmolkit.BioPdbReadError property) (cosmolkit.UffParamError property) line_offset (cosmolkit.SdfReadError property) line_range (cosmolkit.SdfRecordMetadata attribute) LinearDoubleBond (cosmolkit.EmbedFailureCause attribute) LineLengthOutsideBuffer (cosmolkit.PdbRemarkErrorKind attribute) LineNumberOutsideSourceIntRange (cosmolkit.PdbReaderCauseKind attribute) lines_consumed (cosmolkit.SdfRecordStream attribute) link_id (cosmolkit.BioConnection attribute) link_record (cosmolkit.PdbConnectionFinalizationError attribute) LinkIdNotUtf8 (cosmolkit.PdbLinkRecordErrorKind attribute) linking_type (cosmolkit.ResidueInfo attribute) LINKNODES (cosmolkit.CxSmilesFields attribute) LinkRecord (cosmolkit.PdbConnectionFinalizationErrorKind attribute) lipinski_hba() (cosmolkit.Molecule method) lipinski_hbd() (cosmolkit.Molecule method) list (cosmolkit.SelectedSubstanceGroupCopyError property) LLP (cosmolkit.ResidueCode attribute) LMT (cosmolkit.ResidueCode attribute) log (cosmolkit.InchiResult attribute) logical_atom_name (cosmolkit.AtomAddress attribute) logp (cosmolkit.CrippenTotals attribute) LOmega (cosmolkit.BioHelixClass attribute) LonePair (cosmolkit.LigandRef attribute) lower (cosmolkit.AtomRangeBounds attribute) (cosmolkit.AtomRangeDataFunction attribute) Lower (cosmolkit.BoundKind attribute) lower (cosmolkit.PathError property) lower_open (cosmolkit.AtomRangeBounds attribute) (cosmolkit.AtomRangeDataFunction attribute) LowerE (cosmolkit.CipDescriptor attribute) LowerM (cosmolkit.CipDescriptor attribute) LowerP (cosmolkit.CipDescriptor attribute) LowerR (cosmolkit.CipDescriptor attribute) LowerS (cosmolkit.CipDescriptor attribute) LowerZ (cosmolkit.CipDescriptor attribute) LR (cosmolkit.Element attribute) LU (cosmolkit.Element attribute) luzzati_error (cosmolkit.BioRefinementInfo attribute) LV (cosmolkit.Element attribute) LYS (cosmolkit.ResidueCode attribute) M M (cosmolkit.CipDescriptor attribute) m (cosmolkit.CipDescriptor attribute) M2G (cosmolkit.ResidueCode attribute) M3L (cosmolkit.ResidueCode attribute) MA4 (cosmolkit.ResidueCode attribute) MA6 (cosmolkit.ResidueCode attribute) MAA (cosmolkit.ResidueCode attribute) (cosmolkit.ResidueInfoKind attribute) MaccsFingerprintError MaccsFingerprintErrorKind (class in cosmolkit) MaccsFingerprintParams (class in cosmolkit) magnitude (cosmolkit.PropertyIntReadError property) major (cosmolkit.PickleError property) MalformedEntityReference (cosmolkit.XmlParseErrorKind attribute) MalformedGZip (cosmolkit.SvgParseErrorKind attribute) MalformedLine (cosmolkit.UffParamErrorKind attribute) MAN (cosmolkit.ResidueCode attribute) map (cosmolkit.ReactionValidationError property) (cosmolkit.ReactionValidationIssue attribute) map_len (cosmolkit.AlignmentError property) map_number (cosmolkit.CipRankError property) MapOverflow (cosmolkit.ReactionValidationErrorKind attribute) mapped (cosmolkit.MappingValidationError property) (cosmolkit.StereoOrderError property) mapped_atom (cosmolkit.SelectedSubstanceGroupCopyError property) mapped_bond (cosmolkit.SelectedSubstanceGroupCopyError property) MappedBondMissing (cosmolkit.McsErrorKind attribute) Mapping (cosmolkit.DrawingErrorKind attribute) mapping (cosmolkit.HydrogenError property) (cosmolkit.PathError property) Mapping (cosmolkit.PathErrorKind attribute) (cosmolkit.QueryStateErrorKind attribute) mapping (cosmolkit.StereoOrderError property) mapping_len (cosmolkit.TemplateAttachmentOrderError property) mapping_validation (cosmolkit.AtomPathSubsetCopyError property) (cosmolkit.FullCopyComponentError property) MappingContract (cosmolkit.OperationErrorKind attribute) MappingTargetOutOfRange (cosmolkit.TemplateAttachmentOrderErrorKind attribute) MappingValidation (cosmolkit.AtomPathSubsetCopyErrorKind attribute) (cosmolkit.FullCopyComponentErrorKind attribute) MappingValidationError MappingValidationErrorKind (class in cosmolkit) maps (cosmolkit.ReactionValidationIssue attribute) mark_atoms_bonds (cosmolkit.KekulizeParams attribute) Mass (cosmolkit.AtomQueryPredicateKind attribute) MASTER (cosmolkit.PdbWriteFlags attribute) Match (cosmolkit.CrystalffTorsionPreferencesErrorKind attribute) (cosmolkit.DescriptorSearchCauseKind attribute) (cosmolkit.MaccsFingerprintErrorKind attribute) (cosmolkit.PatternFingerprintErrorKind attribute) (cosmolkit.PruningErrorKind attribute) (cosmolkit.TautomerRunErrorKind attribute) (cosmolkit.UffTorsionBondQueryErrorKind attribute) match_chiral_tag (cosmolkit.McsAtomCompareParameters attribute) match_context (cosmolkit.TautomerRunError property) match_error (cosmolkit.TautomerRunError property) match_formal_charge (cosmolkit.McsAtomCompareParameters attribute) match_fused_rings (cosmolkit.McsBondCompareParameters attribute) match_fused_rings_strict (cosmolkit.McsBondCompareParameters attribute) match_isotope (cosmolkit.McsAtomCompareParameters attribute) match_params (cosmolkit.Reaction attribute) match_stereo (cosmolkit.McsBondCompareParameters attribute) match_valences (cosmolkit.McsAtomCompareParameters attribute) MatchArity (cosmolkit.UffTorsionBondQueryErrorKind attribute) MatchAtomIndex (cosmolkit.ReactionRunErrorKind attribute) MatchContext (cosmolkit.TautomerRunErrorKind attribute) MatchError MatchErrorKind (class in cosmolkit) matches() (cosmolkit.ResidueAddress method) matches_without_segment() (cosmolkit.ResidueAddress method) matching (cosmolkit.AlignmentError property) Matching (cosmolkit.AlignmentErrorKind attribute) matching (cosmolkit.CrystalffTorsionPreferencesError property) (cosmolkit.PruningError property) (cosmolkit.ReactionApplyError property) Matching (cosmolkit.ReactionApplyErrorKind attribute) (cosmolkit.ReactionRunErrorKind attribute) MatchingStateLength (cosmolkit.KekulizeErrorKind attribute) MatchResult (class in cosmolkit) MatchTableOutOfRange (cosmolkit.McsErrorKind attribute) Materialization (cosmolkit.BioMmcifReadStage attribute) matrix (cosmolkit.AlignmentTransform attribute) Matrix (cosmolkit.AtomPairErrorKind attribute) matrix (cosmolkit.BioTransform attribute) Matrix (cosmolkit.GraphBoundsErrorKind attribute) (cosmolkit.MorganErrorKind attribute) matrix (cosmolkit.PathError property) Matrix (cosmolkit.PathErrorKind attribute) matrix (cosmolkit.ScaffoldError property) Matrix (cosmolkit.ScaffoldErrorKind attribute) MatrixAxis (class in cosmolkit) MatrixDimensionOverflow (cosmolkit.MatrixErrorKind attribute) MatrixError MatrixErrorKind (class in cosmolkit) MatrixSize (cosmolkit.ScaffoldErrorKind attribute) MatrixSizeMismatch (cosmolkit.ForceFieldKernelErrorKind attribute) max_angle_deg (cosmolkit.ForceFieldAngleConstraintParams attribute) max_backtracks (cosmolkit.KekulizeParams attribute) max_dihedral_deg (cosmolkit.ForceFieldTorsionConstraintParams attribute) max_displacement (cosmolkit.ForceFieldPositionConstraintParams attribute) max_distance (cosmolkit.AtomPairFingerprintParams attribute) (cosmolkit.AtomPairGeneratorParams attribute) (cosmolkit.ForceFieldDistanceConstraintParams attribute) (cosmolkit.McsAtomCompareParameters attribute) max_id (cosmolkit.Coordinate2DError property) (cosmolkit.CoordinateInputError property) (cosmolkit.CoordinateValidationError property) max_isomers (cosmolkit.StereoisomerOptions attribute) max_iterations (cosmolkit.AlignmentParameters attribute) (cosmolkit.BestAlignmentParameters attribute) (cosmolkit.ConformerAlignmentParameters attribute) (cosmolkit.EmbedParams attribute) (cosmolkit.ForceFieldMinimizeParams attribute) (cosmolkit.MmffConformerOptimizationParams attribute) (cosmolkit.MmffOptimizationParams attribute) (cosmolkit.UffConformerOptimizationParams attribute) (cosmolkit.UffOptimizationParams attribute) max_line_length (cosmolkit.BioPdbReadParams attribute) max_matches (cosmolkit.AllConformerRmsdParameters attribute) (cosmolkit.BestAlignmentParameters attribute) (cosmolkit.CoordinateRmsdParameters attribute) (cosmolkit.SubstructMatchParams attribute) max_path (cosmolkit.LayeredFingerprintParams attribute) (cosmolkit.TopologicalFingerprintParams attribute) max_path_length() (cosmolkit.AtomPairsParameters static method) max_products (cosmolkit.ReactionRunParams attribute) max_recursive_iterations (cosmolkit.CipLabelOptions attribute) max_recursive_matches (cosmolkit.SubstructMatchParams attribute) max_tautomers (cosmolkit.TautomerParams attribute) max_transforms (cosmolkit.TautomerParams attribute) maximize_bonds (cosmolkit.McsParameters attribute) maximum (cosmolkit.AromaticityError property) Maximum (cosmolkit.ForceFieldAngleRangeBound attribute) maximum (cosmolkit.StereoOrderError property) maximum_common_substructure() (in module cosmolkit) maximum_common_substructure_with_params() (in module cosmolkit) maximum_supported (cosmolkit.CipRankError property) MaxIterationsExceeded (cosmolkit.CipLabelerErrorKind attribute) MaxTautomersReached (cosmolkit.TautomerEnumerationStatus attribute) MaxTransformsReached (cosmolkit.TautomerEnumerationStatus attribute) MC (cosmolkit.Element attribute) McsAtomComparator (class in cosmolkit) McsAtomCompareParameters (class in cosmolkit) McsBondComparator (class in cosmolkit) McsBondCompareParameters (class in cosmolkit) McsError McsErrorKind (class in cosmolkit) McsParameters (class in cosmolkit) McsProgressError McsProgressErrorKind (class in cosmolkit) McsResult (class in cosmolkit) MD (cosmolkit.Element attribute) Mdl (cosmolkit.AromaticityModel attribute) MDO (cosmolkit.ResidueCode attribute) MEA (cosmolkit.ResidueCode attribute) mean_b (cosmolkit.BioRefinementInfo attribute) mean_i_over_sigma (cosmolkit.BioReflectionsInfo attribute) MED (cosmolkit.ResidueCode attribute) MEN (cosmolkit.ResidueCode attribute) MEQ (cosmolkit.ResidueCode attribute) Mer (cosmolkit.SubstanceGroupKind attribute) merge_hs (cosmolkit.SmartsParseParams attribute) MES (cosmolkit.ResidueCode attribute) message (cosmolkit.AlignmentError property) (cosmolkit.AtropisomerError property) (cosmolkit.BatchError property) (cosmolkit.BondDirectionStereoError property) (cosmolkit.CifReadError property) (cosmolkit.ConformerError property) (cosmolkit.ConformerOptimizerCause attribute) (cosmolkit.CxParseError property) (cosmolkit.CxQueryLoweringError property) (cosmolkit.EnumerationError property) (cosmolkit.GenerationError property) (cosmolkit.GraphBoundsError property) (cosmolkit.InchiDiagnostic attribute) (cosmolkit.InchiResult attribute) (cosmolkit.McsError property) (cosmolkit.McsProgressError property) (cosmolkit.Mol2ReadError property) (cosmolkit.PickleError property) (cosmolkit.PruningError property) (cosmolkit.QueryCompileError property) (cosmolkit.RingFindingError property) (cosmolkit.SdfReadError property) (cosmolkit.SmartsParseError property) (cosmolkit.SmilesParseError property) (cosmolkit.ValenceError property) (cosmolkit.WedgeError property) (cosmolkit.XmlParseError property) (cosmolkit.XyzReadError property) MET (cosmolkit.ResidueCode attribute) metadata (cosmolkit.BioStructure attribute) (cosmolkit.BioStructureParts attribute) metadata() (cosmolkit.SdfDataset method) MetalC (cosmolkit.BioConnectionKind attribute) (cosmolkit.PdbLinkNameCounter attribute) method (cosmolkit.BioExperimentInfo attribute) (cosmolkit.MoleculeOpSpec attribute) MG (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) MG8 (cosmolkit.ResidueCode attribute) MHA (cosmolkit.ResidueCode attribute) MHO (cosmolkit.ResidueCode attribute) MHS (cosmolkit.ResidueCode attribute) MIA (cosmolkit.ResidueCode attribute) min_angle_deg (cosmolkit.ForceFieldAngleConstraintParams attribute) min_dihedral_deg (cosmolkit.ForceFieldTorsionConstraintParams attribute) min_distance (cosmolkit.AtomPairFingerprintParams attribute) (cosmolkit.AtomPairGeneratorParams attribute) (cosmolkit.ForceFieldDistanceConstraintParams attribute) min_path (cosmolkit.LayeredFingerprintParams attribute) (cosmolkit.TopologicalFingerprintParams attribute) min_size (cosmolkit.TopologicalFingerprintParams attribute) Minimization (cosmolkit.EmbedFailureCause attribute) Minimize (cosmolkit.OptimizationStageErrorKind attribute) minimize_() (cosmolkit.MolecularForceField method) MinimizeFourthDimension (cosmolkit.EmbedFailureCause attribute) minimum (cosmolkit.DescriptorError property) Minimum (cosmolkit.ForceFieldAngleRangeBound attribute) minor (cosmolkit.PickleError property) MinRingSize (cosmolkit.AtomRangeDataFunctionKind attribute) (cosmolkit.BondQueryPredicateKind attribute) MismatchedBinArrays (cosmolkit.DescriptorErrorKind attribute) MismatchedTopology (cosmolkit.Coordinate2DLayoutErrorKind attribute) missing (cosmolkit.OperationError property) (cosmolkit.RequiredPropertyStringError property) Missing (cosmolkit.RequiredPropertyStringErrorKind attribute) Missing3DConformer (cosmolkit.CoordinateValidationErrorKind attribute) Missing3dConformer (cosmolkit.MmffBuilderErrorKind attribute) missing_parameters() (cosmolkit.OptimizationOutcome static method) MissingActiveModel (cosmolkit.MmcifAtomSiteGroupingErrorKind attribute) MissingAdditionalOutput (cosmolkit.BatchFingerprintOutputErrorKind attribute) MissingAddressIdentifiers (cosmolkit.MmcifConnectionErrorKind attribute) MissingArenaValue (cosmolkit.MmjsonStructureErrorKind attribute) MissingArrayFirstElement (cosmolkit.MmjsonValueErrorKind attribute) MissingAtom (cosmolkit.NonbondedFragmentMappingErrorKind attribute) MissingAtomMapping (cosmolkit.SelectedSubstanceGroupCopyErrorKind attribute) MissingAtomSiteIdentityField MissingBacktrackAnchor (cosmolkit.KekulizeErrorKind attribute) MissingBondMapping (cosmolkit.SelectedSubstanceGroupCopyErrorKind attribute) MissingCandidateBond (cosmolkit.KekulizeErrorKind attribute) MissingCanonicalChainName (cosmolkit.BioRowChainErrorKind attribute) MissingCapability (cosmolkit.MolPostErrorKind attribute) (cosmolkit.MolWriteErrorKind attribute) (cosmolkit.SdfReadErrorKind attribute) MissingCentralBond (cosmolkit.CrystalffTorsionPreferencesErrorKind attribute) MissingChiralTag (cosmolkit.AtomQueryPredicateKind attribute) MissingComputedScalar (cosmolkit.DescriptorErrorKind attribute) MissingConformer (cosmolkit.MolecularForceFieldErrorKind attribute) (cosmolkit.SearchMcsErrorKind attribute) (cosmolkit.UffEvaluationFailureKind attribute) MissingConformer() (cosmolkit.UffOptimizationErrorKind static method) MissingContinuationTarget (cosmolkit.PdbRemark3ErrorKind attribute) MissingCoordinate (cosmolkit.MolWriteErrorKind attribute) (cosmolkit.PdbWriteErrorKind attribute) MissingCoordinateRow (cosmolkit.FullCopyComponentErrorKind attribute) MissingCoordinates (cosmolkit.Coordinate2DTemplateErrorKind attribute) (cosmolkit.XyzReadErrorKind attribute) MissingCoordinateSelection (cosmolkit.SmilesParseErrorKind attribute) MissingCounter (cosmolkit.EmbedFailureCountErrorKind attribute) MissingCrippenDefaultPattern (cosmolkit.DescriptorErrorKind attribute) MissingCrippenMr (cosmolkit.DescriptorErrorKind attribute) MissingCrippenMrContributions (cosmolkit.DescriptorErrorKind attribute) MissingCurrentDbRef (cosmolkit.PdbDbRefErrorKind attribute) MissingDefaultData (cosmolkit.MmffParamErrorKind attribute) MissingDefinition (cosmolkit.MmffAngleLookupErrorKind attribute) (cosmolkit.MmffOopLookupErrorKind attribute) (cosmolkit.MmffTorLookupErrorKind attribute) MissingEndpointMapping (cosmolkit.SelectedBondCopyErrorKind attribute) MissingEntityMapping (cosmolkit.ProteinProjectionErrorKind attribute) MissingExperimentalRows (cosmolkit.PdbRemark200ErrorKind attribute) MissingExplicitHydrogensError MissingExponent (cosmolkit.JsonErrorKind attribute) MissingFinalHydrogenState (cosmolkit.DescriptorErrorKind attribute) MissingFirstValue (cosmolkit.UnsignedStreamArrayErrorKind attribute) MissingHeader (cosmolkit.MmffVdwParseErrorKind attribute) MissingImplicitHydrogens (cosmolkit.ScaffoldErrorKind attribute) MissingInitializedRings (cosmolkit.DescriptorReadErrorKind attribute) MissingLabuteAsa (cosmolkit.DescriptorErrorKind attribute) MissingLabuteHydrogens (cosmolkit.DescriptorErrorKind attribute) MissingMappedBond (cosmolkit.TautomerRunErrorKind attribute) MissingMatchedBond (cosmolkit.UffTorsionBondQueryErrorKind attribute) MissingModelNumber (cosmolkit.BioRowModelErrorKind attribute) MissingObjectKey (cosmolkit.JsonErrorKind attribute) MissingParameters (cosmolkit.OptimizationStatus attribute) MissingPattern (cosmolkit.MaccsFingerprintErrorKind attribute) MissingPreparedValence (cosmolkit.DescriptorReadErrorKind attribute) (cosmolkit.FingerprintPreparationErrorKind attribute) (cosmolkit.MoleculeHashErrorKind attribute) MissingProbeValue (cosmolkit.StereoOrderErrorKind attribute) MissingProductMapReactant (cosmolkit.ReactionValidationIssueKind attribute) MissingProducts (cosmolkit.ReactionValidationIssueKind attribute) MissingProperty (cosmolkit.ReactionProductErrorKind attribute) MissingPropertyError MissingReactants (cosmolkit.ReactionValidationIssueKind attribute) MissingReactingAtom (cosmolkit.ReactionValidationErrorKind attribute) MissingRecursiveQueryGraph (cosmolkit.SmartsParseErrorKind attribute) MissingRecursiveQueryMolecule (cosmolkit.SmartsWriteErrorKind attribute) MissingRequiredSection (cosmolkit.PickleErrorKind attribute) MissingRingInfo (cosmolkit.ScaffoldErrorKind attribute) (cosmolkit.SearchMcsErrorKind attribute) MissingRootElement (cosmolkit.JsonErrorKind attribute) MissingRow (cosmolkit.FingerprintBatchErrorKind attribute) MissingSmartsPattern (cosmolkit.CrystalffTorsionPreferencesErrorKind attribute) MissingSourceConformerOrder (cosmolkit.CoordinateValidationErrorKind attribute) MissingSourceState (cosmolkit.HydrogenErrorKind attribute) MissingToken (cosmolkit.MmffParamParseCauseKind attribute) MissingValence (cosmolkit.SearchMcsErrorKind attribute) (cosmolkit.TautomerRunErrorKind attribute) MissingValue (cosmolkit.ChemCompAtomErrorKind attribute) (cosmolkit.CifReadErrorKind attribute) misuse_hash (cosmolkit.BioMmcifWriteParams attribute) Mixed (cosmolkit.ChainKind attribute) Mixture (cosmolkit.SubstanceGroupKind attribute) MixtureComponent (cosmolkit.SubstanceGroupKind attribute) MK8 (cosmolkit.ResidueCode attribute) MLE (cosmolkit.ResidueCode attribute) MLU (cosmolkit.ResidueCode attribute) MLY (cosmolkit.ResidueCode attribute) MLZ (cosmolkit.ResidueCode attribute) Mmcif (cosmolkit.BioCoordinateFormat attribute) (cosmolkit.BioReadErrorKind attribute) (cosmolkit.ProteinReadErrorKind attribute) MmcifAssemblyError MmcifAssemblyErrorKind (class in cosmolkit) MmcifAtomSiteGroupingError MmcifAtomSiteGroupingErrorKind (class in cosmolkit) MmcifAtomSiteRowOutOfBounds MmcifAtomSiteScalarError MmcifAtomSiteScalarErrorKind (class in cosmolkit) MmcifCcdRestoreError MmcifCcdRestoreErrorKind (class in cosmolkit) MmcifCisPepError MmcifCisPepErrorKind (class in cosmolkit) MmcifConnectionError MmcifConnectionErrorKind (class in cosmolkit) MmcifCrystalInfoError MmcifCrystalInfoErrorKind (class in cosmolkit) MmcifEntityInfoError MmcifEntityInfoErrorKind (class in cosmolkit) MmcifHelixError MmcifHelixErrorKind (class in cosmolkit) MmcifLabelAddressError MmcifLabelAddressErrorKind (class in cosmolkit) MmcifModResError MmcifModResErrorKind (class in cosmolkit) MmcifOperationExprError MmcifOperationExprErrorKind (class in cosmolkit) MmcifRead (cosmolkit.MolecularIoErrorKind attribute) MmcifSequenceIdError MmcifSequenceIdErrorKind (class in cosmolkit) MmcifSheetError MmcifSheetErrorKind (class in cosmolkit) MmcifSiftsUnpError MmcifSiftsUnpErrorKind (class in cosmolkit) MmcifTlsInfoError MmcifTlsInfoErrorKind (class in cosmolkit) Mmff94 (cosmolkit.AromaticityModel attribute) (cosmolkit.MmffVariant attribute) Mmff94s (cosmolkit.MmffVariant attribute) mmff_energy_gradient() (cosmolkit.Molecule method) mmff_energy_gradient_with_params() (cosmolkit.Molecule method) mmff_force_field() (cosmolkit.Molecule method) mmff_has_all_molecule_params() (cosmolkit.Molecule method) mmff_optimization (cosmolkit.OperationError property) mmff_properties() (cosmolkit.Molecule method) mmff_properties_with_params() (cosmolkit.Molecule method) mmff_variant (cosmolkit.MmffConformerOptimizationParams attribute) (cosmolkit.MmffEvaluationParams attribute) (cosmolkit.MmffForceFieldParams attribute) (cosmolkit.MmffOptimizationParams attribute) (cosmolkit.MmffPropertiesParams attribute) MmffAngleLookupError MmffAngleLookupErrorKind (class in cosmolkit) MmffAtomProperties (class in cosmolkit) MmffBuilderError MmffBuilderErrorKind (class in cosmolkit) MmffConformerOptimizationParams (class in cosmolkit) MmffEnergyGradient (class in cosmolkit) MmffEvaluationParams (class in cosmolkit) MmffForceFieldError MmffForceFieldParams (class in cosmolkit) MmffMolPropertiesError MmffMolPropertiesErrorKind (class in cosmolkit) MmffOopLookupError MmffOopLookupErrorKind (class in cosmolkit) MmffOptimization (cosmolkit.OperationErrorKind attribute) MmffOptimizationError MmffOptimizationFailure MmffOptimizationFailureKind (class in cosmolkit) MmffOptimizationParams (class in cosmolkit) MmffOptimizationSourceError MmffOptimizeMoleculeConfResult (class in cosmolkit) MmffOptimizeMoleculeConfsResult (class in cosmolkit) MmffOptimizeMoleculeResult (class in cosmolkit) MmffParamError MmffParamErrorKind (class in cosmolkit) MmffParamParseCause (class in cosmolkit) MmffParamParseCauseKind (class in cosmolkit) MmffParamParseError MmffParamTable (class in cosmolkit) MmffProperties (class in cosmolkit) MmffPropertiesParams (class in cosmolkit) MmffTorLookupError MmffTorLookupErrorKind (class in cosmolkit) MmffVariant (class in cosmolkit) MmffVdwParseError MmffVdwParseErrorKind (class in cosmolkit) Mmjson (cosmolkit.BioCoordinateFormat attribute) (cosmolkit.BioReadErrorKind attribute) (cosmolkit.PdbInputFormatErrorKind attribute) MmjsonReadError MmjsonReadErrorKind (class in cosmolkit) MmjsonStructureError MmjsonStructureErrorKind (class in cosmolkit) MmjsonUnexpectedType (class in cosmolkit) MmjsonValueError MmjsonValueErrorKind (class in cosmolkit) MN (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) MN3 (cosmolkit.ResidueCode attribute) MO (cosmolkit.Element attribute) mod_id (cosmolkit.BioModRes attribute) mod_res (cosmolkit.PdbReaderCause property) mod_residues (cosmolkit.BioStructure attribute) (cosmolkit.BioStructureParts attribute) model (cosmolkit.AromaticityError property) (cosmolkit.AromaticityParams attribute) Model (cosmolkit.BioRowTraverseErrorKind attribute) model (cosmolkit.ParserCarrierError property) Model (cosmolkit.ParserCarrierErrorKind attribute) model (cosmolkit.PdbStructureFinalizationError attribute) Model (cosmolkit.PdbStructureFinalizationErrorKind attribute) (cosmolkit.ReactionParseErrorKind attribute) model (cosmolkit.SmilesParseError property) Model (cosmolkit.SmilesParseErrorKind attribute) model (cosmolkit.ValenceParams attribute) model() (cosmolkit.BioStructure method) model_count (cosmolkit.PdbModelTransitionError property) model_id (cosmolkit.BioChain attribute) (cosmolkit.BioChainRow attribute) model_num (cosmolkit.BioCisPep attribute) model_transition (cosmolkit.PdbReaderCause property) ModelBuilding (cosmolkit.BioSoftwareClassification attribute) ModelIdOutOfBounds (cosmolkit.PdbModelTransitionErrorKind attribute) ModelNumber (cosmolkit.MmcifAtomSiteGroupingErrorKind attribute) ModelNumberOutsideSourceDefinedRange (cosmolkit.PdbCisPepRecordErrorKind attribute) ModelNumberOutsideSourceIntRange (cosmolkit.PdbModelTransitionErrorKind attribute) models (cosmolkit.BioStructure attribute) (cosmolkit.BioStructureParts attribute) ModelTransition (cosmolkit.PdbReaderCauseKind attribute) ModelWithoutEnd (cosmolkit.PdbModelTransitionErrorKind attribute) Modification (cosmolkit.SubstanceGroupKind attribute) modified_atoms (cosmolkit.TautomerEnumeration attribute) (cosmolkit.TautomerProgress attribute) modified_bonds (cosmolkit.TautomerEnumeration attribute) (cosmolkit.TautomerProgress attribute) ModifiedResidues (cosmolkit.BioMmcifReadStage attribute) modres (cosmolkit.BioMmcifWriteParams attribute) ModRes (cosmolkit.PdbReaderCauseKind attribute) module cosmolkit MOH (cosmolkit.ResidueCode attribute) Mol2Post (cosmolkit.MolecularIoErrorKind attribute) Mol2PostError Mol2Read (cosmolkit.MolecularIoErrorKind attribute) Mol2ReadError Mol2ReadErrorKind (class in cosmolkit) Mol2ReadParams (class in cosmolkit) Mol2Type (class in cosmolkit) mol_from_binary() (in module cosmolkit) mol_from_inchi() (in module cosmolkit) mol_from_mmcif() (in module cosmolkit) mol_from_mol() (in module cosmolkit) mol_from_mol2() (in module cosmolkit) mol_from_pdb() (in module cosmolkit) mol_from_rdkit() (in module cosmolkit) mol_from_sdf() (in module cosmolkit) mol_from_smiles() (in module cosmolkit) mol_from_xyz_block() (in module cosmolkit) mol_properties (cosmolkit.MmffBuilderError property) molar_refractivity (cosmolkit.CrippenTotals attribute) MolBlockWriteParams (class in cosmolkit) MolCoordinateSelection (class in cosmolkit) molecular_formula() (cosmolkit.Molecule method) molecular_formula_with_params() (cosmolkit.Molecule method) molecular_hash() (cosmolkit.Molecule method) molecular_hash_with_ranks() (cosmolkit.Molecule method) molecular_weight() (cosmolkit.Molecule method) molecular_weight_with_params() (cosmolkit.Molecule method) MolecularForceField (class in cosmolkit) MolecularForceFieldErrorKind (class in cosmolkit) MolecularIoError MolecularIoErrorKind (class in cosmolkit) Molecule (class in cosmolkit) molecule (cosmolkit.AtomPairAtomCodeResult attribute) (cosmolkit.EmbedMoleculeResult attribute) (cosmolkit.EmbedMultipleConfsResult attribute) (cosmolkit.MmffOptimizeMoleculeConfsResult attribute) (cosmolkit.MmffOptimizeMoleculeResult attribute) (cosmolkit.ReactionApplyResult attribute) (cosmolkit.SdfRecord attribute) (cosmolkit.UffConformerOptimizationResult attribute) (cosmolkit.UffOptimizationResult attribute) molecule_property (cosmolkit.CipLabelerError property) (cosmolkit.EnumerationError property) (cosmolkit.ReactionProductError property) (cosmolkit.TautomerRunError property) MoleculeAtom (class in cosmolkit) MoleculeBatch (class in cosmolkit) MoleculeBuilder (class in cosmolkit) MoleculeFragmentsError MoleculeFragmentsFailure MoleculeFragmentsFailureKind (class in cosmolkit) MoleculeHashError MoleculeHashErrorKind (class in cosmolkit) MoleculeOpOutput (class in cosmolkit) MoleculeOpSpec (class in cosmolkit) MoleculeProperties (class in cosmolkit) MoleculeProperty (cosmolkit.AtomPathSubsetCopyErrorKind attribute) (cosmolkit.CipLabelerErrorKind attribute) (cosmolkit.CxQueryLoweringErrorKind attribute) (cosmolkit.EnumerationErrorKind attribute) (cosmolkit.Mol2ReadErrorKind attribute) (cosmolkit.MolProcessingErrorKind attribute) (cosmolkit.MorganErrorKind attribute) (cosmolkit.PathErrorKind attribute) (cosmolkit.ReactionProductErrorKind attribute) (cosmolkit.RingFindingErrorKind attribute) (cosmolkit.SanitizeErrorKind attribute) (cosmolkit.SdfReadErrorKind attribute) (cosmolkit.SmartsParseErrorKind attribute) (cosmolkit.SmilesParseErrorKind attribute) (cosmolkit.TautomerRunErrorKind attribute) (cosmolkit.TopologyEditErrorKind attribute) (cosmolkit.XyzReadErrorKind attribute) MoleculePropertyError MoleculePropertyErrorKind (class in cosmolkit) MoleculePropertyWrite (cosmolkit.SmartsWriteErrorKind attribute) MoleculeTransferError MoleculeTransferErrorKind (class in cosmolkit) MOLFILE_VALUES (cosmolkit.CxSmilesFields attribute) MolFileAlias (cosmolkit.AtomQueryPredicateKind attribute) MolFileQueryCode (cosmolkit.BondQueryPredicateKind attribute) MolPost (cosmolkit.SdfReadErrorKind attribute) MolPostError MolPostErrorKind (class in cosmolkit) MolProcessingError MolProcessingErrorKind (class in cosmolkit) MolProperties (cosmolkit.MmffBuilderErrorKind attribute) mols_from_records() (in module cosmolkit) mols_from_sdf_records() (in module cosmolkit) mols_from_smiles_list() (in module cosmolkit) MolWrite (cosmolkit.MolecularIoErrorKind attribute) MolWriteError MolWriteErrorKind (class in cosmolkit) mono_or_laue (cosmolkit.BioDiffractionInfo attribute) monochromator (cosmolkit.BioDiffractionInfo attribute) Monomer (cosmolkit.SubstanceGroupKind attribute) MorganAtomInvariantsGenerator (class in cosmolkit) MorganBondInvariantsGenerator (class in cosmolkit) MorganCallParams (class in cosmolkit) MorganError MorganErrorKind (class in cosmolkit) MorganFingerprintGenerator (class in cosmolkit) MorganFingerprintParams (class in cosmolkit) MorganGeneratorParams (class in cosmolkit) MorganInvariants (class in cosmolkit) MorganReadError MorganReadErrorKind (class in cosmolkit) MorganSettings (class in cosmolkit) move_to_agent_templates (cosmolkit.ReactionTemplateRemovalParams attribute) MPD (cosmolkit.ResidueCode attribute) MPO (cosmolkit.ResidueCode attribute) mqns() (cosmolkit.Molecule method) MRD (cosmolkit.ResidueCode attribute) MRY (cosmolkit.ResidueCode attribute) MSE (cosmolkit.ResidueCode attribute) MT (cosmolkit.Element attribute) MTL (cosmolkit.ResidueCode attribute) mtrix (cosmolkit.PdbReaderCause property) Mtrix (cosmolkit.PdbReaderCauseKind attribute) Multiple (cosmolkit.MoleculeOpOutput attribute) MultipleCharge (cosmolkit.ReactionValidationIssueKind attribute) MultipleFragments (cosmolkit.Coordinate2DTemplateErrorKind attribute) MultipleGroup (cosmolkit.SubstanceGroupKind attribute) MultipleHydrogenCount (cosmolkit.ReactionValidationIssueKind attribute) MultipleImplicitLigands (cosmolkit.StereoOrderErrorKind attribute) MultipleIsotope (cosmolkit.ReactionValidationIssueKind attribute) MultipleMass (cosmolkit.ReactionValidationIssueKind attribute) MultiStep (cosmolkit.ReactionParseErrorKind attribute) murcko_decompose() (cosmolkit.Molecule method) murcko_scaffold() (cosmolkit.Molecule method) MVA (cosmolkit.ResidueCode attribute) N N (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) N8E (cosmolkit.ResidueCode attribute) n_atoms (cosmolkit.UffBuilderError property) n_bits (cosmolkit.AvalonFingerprintParams attribute) (cosmolkit.Fingerprint attribute) (cosmolkit.FingerprintError property) (cosmolkit.MaccsFingerprintParams attribute) (cosmolkit.PatternFingerprintParams attribute) (cosmolkit.SparseBitFingerprint attribute) n_jobs (cosmolkit.BatchExportParams attribute) (cosmolkit.BatchParams attribute) (cosmolkit.BatchQueryParams attribute) NA (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) NAD (cosmolkit.ResidueCode attribute) NAG (cosmolkit.ResidueCode attribute) name (cosmolkit.AdjacencyErrorKind attribute) (cosmolkit.AdjustHsErrorKind attribute) (cosmolkit.AlignmentErrorKind attribute) (cosmolkit.AromaticityErrorKind attribute) (cosmolkit.AromaticityModel attribute) (cosmolkit.AtomCodeErrorKind attribute) (cosmolkit.AtomCodeExplanationErrorKind attribute) (cosmolkit.AtomPairErrorKind attribute) (cosmolkit.AtomPairReadErrorKind attribute) (cosmolkit.AtomPathSubsetCopyErrorKind attribute) (cosmolkit.AtomPropertyErrorKind attribute) (cosmolkit.AtomPropertyReadErrorKind attribute) (cosmolkit.AtomQueryPredicate attribute) (cosmolkit.AtomQueryPredicateKind attribute) (cosmolkit.AtomRangeBoundsKind attribute) (cosmolkit.AtomRangeDataFunctionKind attribute) (cosmolkit.AtomSiteIdentityField attribute) (cosmolkit.AtropisomerErrorKind attribute) (cosmolkit.AttachmentExpansionErrorKind attribute) (cosmolkit.AutomaticForceFieldConstructionErrorKind attribute) (cosmolkit.AvalonEngineErrorKind attribute) (cosmolkit.AvalonFingerprintErrorKind attribute) (cosmolkit.BatchErrorMode attribute) (cosmolkit.BatchFingerprintOutputErrorKind attribute) (cosmolkit.BatchImageErrorKind attribute) (cosmolkit.BioAssembly attribute) (cosmolkit.BioAssemblyOperator attribute) (cosmolkit.BioAssemblySpecialKind attribute) (cosmolkit.BioAsu attribute) (cosmolkit.BioAtom attribute) (cosmolkit.BioAtomRow attribute) (cosmolkit.BioCalcFlag attribute) (cosmolkit.BioConnection attribute) (cosmolkit.BioConnectionKind attribute) (cosmolkit.BioCoordinateFormat attribute) (cosmolkit.BioHelixClass attribute) (cosmolkit.BioMmcifReadStage attribute) (cosmolkit.BioMmcifWriteErrorKind attribute) (cosmolkit.BioMoleculeConversionErrorKind attribute) (cosmolkit.BioMoleculeErrorKind attribute) (cosmolkit.BioOperationErrorKind attribute) (cosmolkit.BioPdbReadStage attribute) (cosmolkit.BioPdbWriteErrorKind attribute) (cosmolkit.BioReadErrorKind attribute) (cosmolkit.BioRefinementRestraint attribute) (cosmolkit.BioResidue attribute) (cosmolkit.BioResidueRow attribute) (cosmolkit.BioRowChainErrorKind attribute) (cosmolkit.BioRowModelErrorKind attribute) (cosmolkit.BioRowTraverseErrorKind attribute) (cosmolkit.BioSelectionCopyCauseKind attribute) (cosmolkit.BioSelectionParseErrorKind attribute) (cosmolkit.BioSheet attribute) (cosmolkit.BioSoftwareClassification attribute) (cosmolkit.BioSoftwareItem attribute) (cosmolkit.BioStrand attribute) (cosmolkit.BioStructure attribute) (cosmolkit.BioStructureErrorKind attribute) (cosmolkit.BioStructureSourceState attribute) (cosmolkit.BondDirection attribute) (cosmolkit.BondDirectionStereoErrorKind attribute) (cosmolkit.BondEndPointsParseErrorKind attribute) (cosmolkit.BondOrder attribute) (cosmolkit.BondQueryPredicate attribute) (cosmolkit.BondQueryPredicateKind attribute) (cosmolkit.BondStereo attribute) (cosmolkit.BondValueErrorKind attribute) (cosmolkit.BoundKind attribute) (cosmolkit.BoundsMatrixErrorKind attribute) (cosmolkit.BoundsQueryErrorKind attribute) (cosmolkit.CanonicalRankErrorKind attribute) (cosmolkit.ChainKind attribute) (cosmolkit.ChemCompAtomErrorKind attribute) (cosmolkit.ChemCompModelErrorKind attribute) (cosmolkit.ChemistryProblemErrorKind attribute) (cosmolkit.ChiralTag attribute) (cosmolkit.CifReadErrorKind attribute) (cosmolkit.CipDescriptor attribute) (cosmolkit.CipDescriptorErrorKind attribute) (cosmolkit.CipLabelerErrorKind attribute) (cosmolkit.CipRankErrorKind attribute) (cosmolkit.CleanupErrorKind attribute) (cosmolkit.ConformerErrorKind attribute) (cosmolkit.ConformerOptimizerCauseKind attribute) (cosmolkit.ConjugationErrorKind attribute) (cosmolkit.Coordinate2DErrorKind attribute) (cosmolkit.Coordinate2DLayoutErrorKind attribute) (cosmolkit.Coordinate2DTemplateErrorKind attribute) (cosmolkit.Coordinate3DReadErrorKind attribute) (cosmolkit.CoordinateBlockSelectionErrorKind attribute) (cosmolkit.CoordinateDimension attribute) (cosmolkit.CoordinateInputErrorKind attribute) (cosmolkit.CoordinateValidationErrorKind attribute) (cosmolkit.CoordinateZPolicy attribute) (cosmolkit.CrystalffTorsionPreferencesErrorKind attribute) (cosmolkit.CxQueryLoweringErrorKind attribute) (cosmolkit.CxStereoGroupMergeErrorKind attribute) (cosmolkit.DescriptorErrorKind attribute) (cosmolkit.DescriptorReadErrorKind attribute) (cosmolkit.DescriptorSearchCauseKind attribute) (cosmolkit.DispatchedUffOptimizationErrorKind attribute) (cosmolkit.DistGeomForceFieldErrorKind attribute) (cosmolkit.DoubleBondStereoErrorKind attribute) (cosmolkit.DoubleLexicalReadErrorKind attribute) (cosmolkit.DrawingErrorKind attribute) (cosmolkit.DrawingWriteErrorKind attribute) (cosmolkit.EmbedFailureCause attribute) (cosmolkit.EmbedFailureCountErrorKind attribute) (cosmolkit.EmbedSeedErrorKind attribute) (cosmolkit.EmbedTermination attribute) (cosmolkit.EntityKind attribute) (cosmolkit.EnumerationErrorKind attribute) (cosmolkit.FeatureSpec attribute) (cosmolkit.FingerprintBatchErrorKind attribute) (cosmolkit.FingerprintErrorKind attribute) (cosmolkit.FingerprintJsonErrorKind attribute) (cosmolkit.FingerprintPreparationErrorKind attribute) (cosmolkit.FingerprintWorkerErrorKind attribute) (cosmolkit.ForceFieldAngleIndexArgument attribute) (cosmolkit.ForceFieldAngleRangeBound attribute) (cosmolkit.ForceFieldBondIndexArgument attribute) (cosmolkit.ForceFieldConstructionErrorKind attribute) (cosmolkit.ForceFieldIndexArgument attribute) (cosmolkit.ForceFieldKernelErrorKind attribute) (cosmolkit.ForceFieldTorsionIndexArgument attribute) (cosmolkit.FragmentCoordinateViewErrorKind attribute) (cosmolkit.FragmentWriteInputErrorKind attribute) (cosmolkit.FullCopyComponentErrorKind attribute) (cosmolkit.GenerationErrorKind attribute) (cosmolkit.GenerationFailureKind attribute) (cosmolkit.GraphBoundsErrorKind attribute) (cosmolkit.Hybridization attribute) (cosmolkit.HybridizationErrorKind attribute) (cosmolkit.HydrogenError property) (cosmolkit.HydrogenErrorKind attribute) (cosmolkit.InchiDiagnosticLevel attribute) (cosmolkit.InchiErrorKind attribute) (cosmolkit.JsonErrorKind attribute) (cosmolkit.KekulizeErrorKind attribute) (cosmolkit.LayeredFingerprintErrorKind attribute) (cosmolkit.LegacyStereoErrorKind attribute) (cosmolkit.MaccsFingerprintErrorKind attribute) (cosmolkit.MappingValidationErrorKind attribute) (cosmolkit.MatchErrorKind attribute) (cosmolkit.MatrixAxis attribute) (cosmolkit.MatrixErrorKind attribute) (cosmolkit.McsAtomComparator attribute) (cosmolkit.McsBondComparator attribute) (cosmolkit.McsErrorKind attribute) (cosmolkit.McsProgressErrorKind attribute) (cosmolkit.MmcifAssemblyErrorKind attribute) (cosmolkit.MmcifAtomSiteGroupingErrorKind attribute) (cosmolkit.MmcifAtomSiteScalarErrorKind attribute) (cosmolkit.MmcifCcdRestoreErrorKind attribute) (cosmolkit.MmcifCisPepErrorKind attribute) (cosmolkit.MmcifConnectionErrorKind attribute) (cosmolkit.MmcifCrystalInfoErrorKind attribute) (cosmolkit.MmcifEntityInfoErrorKind attribute) (cosmolkit.MmcifHelixErrorKind attribute) (cosmolkit.MmcifLabelAddressErrorKind attribute) (cosmolkit.MmcifModResErrorKind attribute) (cosmolkit.MmcifOperationExprErrorKind attribute) (cosmolkit.MmcifSequenceIdErrorKind attribute) (cosmolkit.MmcifSheetErrorKind attribute) (cosmolkit.MmcifSiftsUnpErrorKind attribute) (cosmolkit.MmcifTlsInfoErrorKind attribute) (cosmolkit.MmffAngleLookupErrorKind attribute) (cosmolkit.MmffBuilderErrorKind attribute) (cosmolkit.MmffMolPropertiesErrorKind attribute) (cosmolkit.MmffOopLookupErrorKind attribute) (cosmolkit.MmffOptimizationFailureKind attribute) (cosmolkit.MmffParamErrorKind attribute) (cosmolkit.MmffParamParseCauseKind attribute) (cosmolkit.MmffParamTable attribute) (cosmolkit.MmffTorLookupErrorKind attribute) (cosmolkit.MmffVariant attribute) (cosmolkit.MmffVdwParseErrorKind attribute) (cosmolkit.MmjsonReadErrorKind attribute) (cosmolkit.MmjsonStructureErrorKind attribute) (cosmolkit.MmjsonUnexpectedType attribute) (cosmolkit.MmjsonValueErrorKind attribute) (cosmolkit.Mol2ReadErrorKind attribute) (cosmolkit.Mol2Type attribute) (cosmolkit.MolecularForceFieldErrorKind attribute) (cosmolkit.MolecularIoError property) (cosmolkit.MolecularIoErrorKind attribute) (cosmolkit.MoleculeFragmentsFailureKind attribute) (cosmolkit.MoleculeHashErrorKind attribute) (cosmolkit.MoleculeOpOutput attribute) (cosmolkit.MoleculeProperties attribute) (cosmolkit.MoleculePropertyErrorKind attribute) (cosmolkit.MoleculeTransferErrorKind attribute) (cosmolkit.MolPostErrorKind attribute) (cosmolkit.MolProcessingErrorKind attribute) (cosmolkit.MolWriteErrorKind attribute) (cosmolkit.MorganErrorKind attribute) (cosmolkit.MorganReadErrorKind attribute) (cosmolkit.NonbondedAssemblyErrorKind attribute) (cosmolkit.NonbondedFragmentMappingErrorKind attribute) (cosmolkit.OperationError property) (cosmolkit.OperationErrorKind attribute) (cosmolkit.OptimizationStageErrorKind attribute) (cosmolkit.OptimizationStatus attribute) (cosmolkit.OrderedFragmentBuildErrorKind attribute) (cosmolkit.ParityPolicy attribute) (cosmolkit.ParserCarrierErrorKind attribute) (cosmolkit.ParserStereoOrderErrorKind attribute) (cosmolkit.PathErrorKind attribute) (cosmolkit.PatternFingerprintErrorKind attribute) (cosmolkit.PdbAtomFieldErrorKind attribute) (cosmolkit.PdbCisPepRecordErrorKind attribute) (cosmolkit.PdbConectErrorKind attribute) (cosmolkit.PdbConnectionFinalizationErrorKind attribute) (cosmolkit.PdbCrystalErrorKind attribute) (cosmolkit.PdbDbRefErrorKind attribute) (cosmolkit.PdbHeaderErrorKind attribute) (cosmolkit.PdbHelixErrorKind attribute) (cosmolkit.PdbInputFormatErrorKind attribute) (cosmolkit.PdbLinkNameCounter attribute) (cosmolkit.PdbLinkRecordErrorKind attribute) (cosmolkit.PdbModelTransitionErrorKind attribute) (cosmolkit.PdbModResErrorKind attribute) (cosmolkit.PdbMtrixErrorKind attribute) (cosmolkit.PdbPostprocessErrorKind attribute) (cosmolkit.PdbReaderCauseKind attribute) (cosmolkit.PdbRemark200ErrorKind attribute) (cosmolkit.PdbRemark350ErrorKind attribute) (cosmolkit.PdbRemark3ErrorKind attribute) (cosmolkit.PdbRemarkErrorKind attribute) (cosmolkit.PdbRemarkFinalizationErrorKind attribute) (cosmolkit.PdbRemarkMetadataErrorKind attribute) (cosmolkit.PdbResidueKeyErrorKind attribute) (cosmolkit.PdbSheetErrorKind attribute) (cosmolkit.PdbSsbondRecordErrorKind attribute) (cosmolkit.PdbStructureFinalizationErrorKind attribute) (cosmolkit.PdbWriteErrorKind attribute) (cosmolkit.PeriodicTableErrorKind attribute) (cosmolkit.PickleErrorKind attribute) (cosmolkit.PolymerKind attribute) (cosmolkit.PotentialStereoDescriptor attribute) (cosmolkit.PotentialStereoErrorKind attribute) (cosmolkit.PotentialStereoSpecified attribute) (cosmolkit.PotentialStereoType attribute) (cosmolkit.PropertyCacheErrorKind attribute) (cosmolkit.PropertyIntReadErrorKind attribute) (cosmolkit.PropertyStringErrorKind attribute) (cosmolkit.PropertyUIntReadErrorKind attribute) (cosmolkit.PropertyULongReadErrorKind attribute) (cosmolkit.PropertyValueKind attribute) (cosmolkit.ProteinAtomRef attribute) (cosmolkit.ProteinProjectionErrorKind attribute) (cosmolkit.ProteinReadErrorKind attribute) (cosmolkit.ProteinResidueRef attribute) (cosmolkit.PruningErrorKind attribute) (cosmolkit.QueryAtomConversionErrorKind attribute) (cosmolkit.QueryCompileErrorKind attribute) (cosmolkit.QueryGraph attribute) (cosmolkit.QueryGraphErrorKind attribute) (cosmolkit.QueryMatchContextErrorKind attribute) (cosmolkit.QueryStateErrorKind attribute) (cosmolkit.RadicalErrorKind attribute) (cosmolkit.ReactionApplyErrorKind attribute) (cosmolkit.ReactionInitializationErrorKind attribute) (cosmolkit.ReactionModelErrorKind attribute) (cosmolkit.ReactionParseErrorKind attribute) (cosmolkit.ReactionProductErrorKind attribute) (cosmolkit.ReactionRole attribute) (cosmolkit.ReactionRunErrorKind attribute) (cosmolkit.ReactionValidationErrorKind attribute) (cosmolkit.ReactionValidationIssueKind attribute) (cosmolkit.ReactionValidationSeverity attribute) (cosmolkit.ReactionWriteErrorKind attribute) (cosmolkit.RequiredPropertyStringErrorKind attribute) (cosmolkit.ResidueAddress attribute) (cosmolkit.ResidueCode attribute) (cosmolkit.ResidueIdentity attribute) (cosmolkit.ResidueInfo attribute) (cosmolkit.ResidueInfoKind attribute) (cosmolkit.ResidueKind attribute) (cosmolkit.ResidueSequenceErrorKind attribute) (cosmolkit.RingDecomposerErrorKind attribute) (cosmolkit.RingFindingErrorKind attribute) (cosmolkit.RotatableBondsOptions attribute) (cosmolkit.SanitizeErrorKind attribute) (cosmolkit.SanitizeStage attribute) (cosmolkit.ScaffoldErrorKind attribute) (cosmolkit.SdfCoordinateMode attribute) (cosmolkit.SdfErrorKind attribute) (cosmolkit.SdfFormat attribute) (cosmolkit.SdfPropertyList attribute) (cosmolkit.SdfPropertyListTarget attribute) (cosmolkit.SdfReadError property) (cosmolkit.SdfReadErrorKind attribute) (cosmolkit.SdfWriteErrorKind attribute) (cosmolkit.SearchMcsErrorKind attribute) (cosmolkit.SelectedBondCopyErrorKind attribute) (cosmolkit.SelectedSubstanceGroupCopyErrorKind attribute) (cosmolkit.SerdeJsonCategory attribute) (cosmolkit.SerialConformerOptimizationErrorKind attribute) (cosmolkit.SerialUffOptimizationErrorKind attribute) (cosmolkit.SingleConformerOptimizationErrorKind attribute) (cosmolkit.SmartsParseErrorKind attribute) (cosmolkit.SmartsTraversalErrorKind attribute) (cosmolkit.SmartsWriteErrorKind attribute) (cosmolkit.SmilesErrorKind attribute) (cosmolkit.SmilesParseErrorKind attribute) (cosmolkit.SmilesStereoErrorKind attribute) (cosmolkit.SmilesWriteErrorKind attribute) (cosmolkit.StereoErrorKind attribute) (cosmolkit.StereoGroupErrorKind attribute) (cosmolkit.StereoGroupKind attribute) (cosmolkit.StereoOrderErrorKind attribute) (cosmolkit.StereoReadErrorKind attribute) (cosmolkit.SubstanceGroupAtomList attribute) (cosmolkit.SubstructMatchErrorKind attribute) (cosmolkit.SvgParseErrorKind attribute) (cosmolkit.TautomerCatalogErrorKind attribute) (cosmolkit.TautomerEnumerationStatus attribute) (cosmolkit.TautomerRunErrorKind attribute) (cosmolkit.TautomerScoreTerm attribute) (cosmolkit.TautomerTransformErrorKind attribute) (cosmolkit.TemplateAttachmentOrderErrorKind attribute) (cosmolkit.ThreadCountErrorKind attribute) (cosmolkit.TopologicalFingerprintErrorKind attribute) (cosmolkit.TopologicalTorsionErrorKind attribute) (cosmolkit.TopologicalTorsionPathScoreErrorKind attribute) (cosmolkit.TopologicalTorsionReadErrorKind attribute) (cosmolkit.TopologyEditErrorKind attribute) (cosmolkit.TopologyValidationErrorKind attribute) (cosmolkit.TransformErrorKind attribute) (cosmolkit.UffBondMathErrorKind attribute) (cosmolkit.UffBoundsCauseKind attribute) (cosmolkit.UffBuilderErrorKind attribute) (cosmolkit.UffDefaultTorsionQueryErrorKind attribute) (cosmolkit.UffEvaluationFailureKind attribute) (cosmolkit.UffInversionContributionErrorKind attribute) (cosmolkit.UffInversionIndexArgument attribute) (cosmolkit.UffParamErrorKind attribute) (cosmolkit.UffParameterErrorKind attribute) (cosmolkit.UffParameterQueryErrorKind attribute) (cosmolkit.UffPreparedOptimizationErrorKind attribute) (cosmolkit.UffPreparedValenceField attribute) (cosmolkit.UffThreadCountErrorKind attribute) (cosmolkit.UffTorsionBondQueryErrorKind attribute) (cosmolkit.UffTypingErrorKind attribute) (cosmolkit.UffTypingInput attribute) (cosmolkit.UIntLexicalReadErrorKind attribute) (cosmolkit.UnsignedStreamArrayErrorKind attribute) (cosmolkit.ValenceErrorKind attribute) (cosmolkit.ValenceModel attribute) (cosmolkit.ValencePhase attribute) (cosmolkit.WedgeErrorKind attribute) (cosmolkit.XmlParseErrorKind attribute) (cosmolkit.XyzReadErrorKind attribute) (cosmolkit.XyzWriteErrorKind attribute) NameCounterOutsideSourceDefinedRange (cosmolkit.PdbLinkRecordErrorKind attribute) NameOutsideCanonicalBoundary (cosmolkit.ChemCompAtomErrorKind attribute) names (cosmolkit.AdjacencyErrorKind attribute) (cosmolkit.AdjustHsErrorKind attribute) (cosmolkit.AlignmentErrorKind attribute) (cosmolkit.AromaticityErrorKind attribute) (cosmolkit.AromaticityModel attribute) (cosmolkit.AtomCodeErrorKind attribute) (cosmolkit.AtomCodeExplanationErrorKind attribute) (cosmolkit.AtomPairErrorKind attribute) (cosmolkit.AtomPairReadErrorKind attribute) (cosmolkit.AtomPathSubsetCopyErrorKind attribute) (cosmolkit.AtomPropertyErrorKind attribute) (cosmolkit.AtomPropertyReadErrorKind attribute) (cosmolkit.AtomQueryPredicateKind attribute) (cosmolkit.AtomRangeBoundsKind attribute) (cosmolkit.AtomRangeDataFunctionKind attribute) (cosmolkit.AtomSiteIdentityField attribute) (cosmolkit.AtropisomerErrorKind attribute) (cosmolkit.AttachmentExpansionErrorKind attribute) (cosmolkit.AutomaticForceFieldConstructionErrorKind attribute) (cosmolkit.AvalonEngineErrorKind attribute) (cosmolkit.AvalonFingerprintErrorKind attribute) (cosmolkit.BatchErrorMode attribute) (cosmolkit.BatchFingerprintOutputErrorKind attribute) (cosmolkit.BatchImageErrorKind attribute) (cosmolkit.BioAssemblySpecialKind attribute) (cosmolkit.BioAsu attribute) (cosmolkit.BioCalcFlag attribute) (cosmolkit.BioConnectionKind attribute) (cosmolkit.BioCoordinateFormat attribute) (cosmolkit.BioHelixClass attribute) (cosmolkit.BioMmcifReadStage attribute) (cosmolkit.BioMmcifWriteErrorKind attribute) (cosmolkit.BioMoleculeConversionErrorKind attribute) (cosmolkit.BioMoleculeErrorKind attribute) (cosmolkit.BioOperationErrorKind attribute) (cosmolkit.BioPdbReadStage attribute) (cosmolkit.BioPdbWriteErrorKind attribute) (cosmolkit.BioReadErrorKind attribute) (cosmolkit.BioRowChainErrorKind attribute) (cosmolkit.BioRowModelErrorKind attribute) (cosmolkit.BioRowTraverseErrorKind attribute) (cosmolkit.BioSelectionCopyCauseKind attribute) (cosmolkit.BioSelectionParseErrorKind attribute) (cosmolkit.BioSoftwareClassification attribute) (cosmolkit.BioStructureErrorKind attribute) (cosmolkit.BondDirection attribute) (cosmolkit.BondDirectionStereoErrorKind attribute) (cosmolkit.BondEndPointsParseErrorKind attribute) (cosmolkit.BondOrder attribute) (cosmolkit.BondQueryPredicateKind attribute) (cosmolkit.BondStereo attribute) (cosmolkit.BondValueErrorKind attribute) (cosmolkit.BoundKind attribute) (cosmolkit.BoundsMatrixErrorKind attribute) (cosmolkit.BoundsQueryErrorKind attribute) (cosmolkit.CanonicalRankErrorKind attribute) (cosmolkit.ChainKind attribute) (cosmolkit.ChemCompAtomErrorKind attribute) (cosmolkit.ChemCompModelErrorKind attribute) (cosmolkit.ChemistryProblemErrorKind attribute) (cosmolkit.ChiralTag attribute) (cosmolkit.CifReadErrorKind attribute) (cosmolkit.CipDescriptor attribute) (cosmolkit.CipDescriptorErrorKind attribute) (cosmolkit.CipLabelerErrorKind attribute) (cosmolkit.CipRankErrorKind attribute) (cosmolkit.CleanupErrorKind attribute) (cosmolkit.ConformerErrorKind attribute) (cosmolkit.ConformerOptimizerCauseKind attribute) (cosmolkit.ConjugationErrorKind attribute) (cosmolkit.Coordinate2DErrorKind attribute) (cosmolkit.Coordinate2DLayoutErrorKind attribute) (cosmolkit.Coordinate2DTemplateErrorKind attribute) (cosmolkit.Coordinate3DReadErrorKind attribute) (cosmolkit.CoordinateBlockSelectionErrorKind attribute) (cosmolkit.CoordinateDimension attribute) (cosmolkit.CoordinateInputErrorKind attribute) (cosmolkit.CoordinateValidationErrorKind attribute) (cosmolkit.CoordinateZPolicy attribute) (cosmolkit.CrystalffTorsionPreferencesErrorKind attribute) (cosmolkit.CxQueryLoweringErrorKind attribute) (cosmolkit.CxStereoGroupMergeErrorKind attribute) (cosmolkit.DescriptorErrorKind attribute) (cosmolkit.DescriptorReadErrorKind attribute) (cosmolkit.DescriptorSearchCauseKind attribute) (cosmolkit.DispatchedUffOptimizationErrorKind attribute) (cosmolkit.DistGeomForceFieldErrorKind attribute) (cosmolkit.DoubleBondStereoErrorKind attribute) (cosmolkit.DoubleLexicalReadErrorKind attribute) (cosmolkit.DrawingErrorKind attribute) (cosmolkit.DrawingWriteErrorKind attribute) (cosmolkit.EmbedFailureCause attribute) (cosmolkit.EmbedFailureCountErrorKind attribute) (cosmolkit.EmbedSeedErrorKind attribute) (cosmolkit.EmbedTermination attribute) (cosmolkit.EntityKind attribute) (cosmolkit.EnumerationErrorKind attribute) (cosmolkit.FingerprintBatchErrorKind attribute) (cosmolkit.FingerprintErrorKind attribute) (cosmolkit.FingerprintJsonErrorKind attribute) (cosmolkit.FingerprintPreparationErrorKind attribute) (cosmolkit.FingerprintWorkerErrorKind attribute) (cosmolkit.ForceFieldAngleIndexArgument attribute) (cosmolkit.ForceFieldAngleRangeBound attribute) (cosmolkit.ForceFieldBondIndexArgument attribute) (cosmolkit.ForceFieldConstructionErrorKind attribute) (cosmolkit.ForceFieldIndexArgument attribute) (cosmolkit.ForceFieldKernelErrorKind attribute) (cosmolkit.ForceFieldTorsionIndexArgument attribute) (cosmolkit.FragmentCoordinateViewErrorKind attribute) (cosmolkit.FragmentWriteInputErrorKind attribute) (cosmolkit.FullCopyComponentErrorKind attribute) (cosmolkit.GenerationErrorKind attribute) (cosmolkit.GenerationFailureKind attribute) (cosmolkit.GraphBoundsErrorKind attribute) (cosmolkit.Hybridization attribute) (cosmolkit.HybridizationErrorKind attribute) (cosmolkit.HydrogenErrorKind attribute) (cosmolkit.InchiDiagnosticLevel attribute) (cosmolkit.InchiErrorKind attribute) (cosmolkit.JsonErrorKind attribute) (cosmolkit.KekulizeErrorKind attribute) (cosmolkit.LayeredFingerprintErrorKind attribute) (cosmolkit.LegacyStereoErrorKind attribute) (cosmolkit.MaccsFingerprintErrorKind attribute) (cosmolkit.MappingValidationErrorKind attribute) (cosmolkit.MatchErrorKind attribute) (cosmolkit.MatrixAxis attribute) (cosmolkit.MatrixErrorKind attribute) (cosmolkit.McsAtomComparator attribute) (cosmolkit.McsBondComparator attribute) (cosmolkit.McsErrorKind attribute) (cosmolkit.McsProgressErrorKind attribute) (cosmolkit.MmcifAssemblyErrorKind attribute) (cosmolkit.MmcifAtomSiteGroupingErrorKind attribute) (cosmolkit.MmcifAtomSiteScalarErrorKind attribute) (cosmolkit.MmcifCcdRestoreErrorKind attribute) (cosmolkit.MmcifCisPepErrorKind attribute) (cosmolkit.MmcifConnectionErrorKind attribute) (cosmolkit.MmcifCrystalInfoErrorKind attribute) (cosmolkit.MmcifEntityInfoErrorKind attribute) (cosmolkit.MmcifHelixErrorKind attribute) (cosmolkit.MmcifLabelAddressErrorKind attribute) (cosmolkit.MmcifModResErrorKind attribute) (cosmolkit.MmcifOperationExprErrorKind attribute) (cosmolkit.MmcifSequenceIdErrorKind attribute) (cosmolkit.MmcifSheetErrorKind attribute) (cosmolkit.MmcifSiftsUnpErrorKind attribute) (cosmolkit.MmcifTlsInfoErrorKind attribute) (cosmolkit.MmffAngleLookupErrorKind attribute) (cosmolkit.MmffBuilderErrorKind attribute) (cosmolkit.MmffMolPropertiesErrorKind attribute) (cosmolkit.MmffOopLookupErrorKind attribute) (cosmolkit.MmffOptimizationFailureKind attribute) (cosmolkit.MmffParamErrorKind attribute) (cosmolkit.MmffParamParseCauseKind attribute) (cosmolkit.MmffParamTable attribute) (cosmolkit.MmffTorLookupErrorKind attribute) (cosmolkit.MmffVariant attribute) (cosmolkit.MmffVdwParseErrorKind attribute) (cosmolkit.MmjsonReadErrorKind attribute) (cosmolkit.MmjsonStructureErrorKind attribute) (cosmolkit.MmjsonUnexpectedType attribute) (cosmolkit.MmjsonValueErrorKind attribute) (cosmolkit.Mol2ReadErrorKind attribute) (cosmolkit.Mol2Type attribute) (cosmolkit.MolecularForceFieldErrorKind attribute) (cosmolkit.MolecularIoErrorKind attribute) (cosmolkit.MoleculeFragmentsFailureKind attribute) (cosmolkit.MoleculeHashErrorKind attribute) (cosmolkit.MoleculeOpOutput attribute) (cosmolkit.MoleculePropertyErrorKind attribute) (cosmolkit.MoleculeTransferErrorKind attribute) (cosmolkit.MolPostErrorKind attribute) (cosmolkit.MolProcessingErrorKind attribute) (cosmolkit.MolWriteErrorKind attribute) (cosmolkit.MorganErrorKind attribute) (cosmolkit.MorganReadErrorKind attribute) (cosmolkit.NonbondedAssemblyErrorKind attribute) (cosmolkit.NonbondedFragmentMappingErrorKind attribute) (cosmolkit.OperationErrorKind attribute) (cosmolkit.OptimizationStageErrorKind attribute) (cosmolkit.OptimizationStatus attribute) (cosmolkit.OrderedFragmentBuildErrorKind attribute) (cosmolkit.ParityPolicy attribute) (cosmolkit.ParserCarrierErrorKind attribute) (cosmolkit.ParserStereoOrderErrorKind attribute) (cosmolkit.PathErrorKind attribute) (cosmolkit.PatternFingerprintErrorKind attribute) (cosmolkit.PdbAtomFieldErrorKind attribute) (cosmolkit.PdbCisPepRecordErrorKind attribute) (cosmolkit.PdbConectErrorKind attribute) (cosmolkit.PdbConnectionFinalizationErrorKind attribute) (cosmolkit.PdbCrystalErrorKind attribute) (cosmolkit.PdbDbRefErrorKind attribute) (cosmolkit.PdbHeaderErrorKind attribute) (cosmolkit.PdbHelixErrorKind attribute) (cosmolkit.PdbInputFormatErrorKind attribute) (cosmolkit.PdbLinkNameCounter attribute) (cosmolkit.PdbLinkRecordErrorKind attribute) (cosmolkit.PdbModelTransitionErrorKind attribute) (cosmolkit.PdbModResErrorKind attribute) (cosmolkit.PdbMtrixErrorKind attribute) (cosmolkit.PdbPostprocessErrorKind attribute) (cosmolkit.PdbReaderCauseKind attribute) (cosmolkit.PdbRemark200ErrorKind attribute) (cosmolkit.PdbRemark350ErrorKind attribute) (cosmolkit.PdbRemark3ErrorKind attribute) (cosmolkit.PdbRemarkErrorKind attribute) (cosmolkit.PdbRemarkFinalizationErrorKind attribute) (cosmolkit.PdbRemarkMetadataErrorKind attribute) (cosmolkit.PdbResidueKeyErrorKind attribute) (cosmolkit.PdbSheetErrorKind attribute) (cosmolkit.PdbSsbondRecordErrorKind attribute) (cosmolkit.PdbStructureFinalizationErrorKind attribute) (cosmolkit.PdbWriteErrorKind attribute) (cosmolkit.PeriodicTableErrorKind attribute) (cosmolkit.PickleErrorKind attribute) (cosmolkit.PolymerKind attribute) (cosmolkit.PotentialStereoDescriptor attribute) (cosmolkit.PotentialStereoErrorKind attribute) (cosmolkit.PotentialStereoSpecified attribute) (cosmolkit.PotentialStereoType attribute) (cosmolkit.PropertyCacheErrorKind attribute) (cosmolkit.PropertyIntReadErrorKind attribute) (cosmolkit.PropertyStringErrorKind attribute) (cosmolkit.PropertyUIntReadErrorKind attribute) (cosmolkit.PropertyULongReadErrorKind attribute) (cosmolkit.PropertyValueKind attribute) (cosmolkit.ProteinProjectionErrorKind attribute) (cosmolkit.ProteinReadErrorKind attribute) (cosmolkit.PruningErrorKind attribute) (cosmolkit.QueryAtomConversionErrorKind attribute) (cosmolkit.QueryCompileErrorKind attribute) (cosmolkit.QueryGraphErrorKind attribute) (cosmolkit.QueryMatchContextErrorKind attribute) (cosmolkit.QueryStateErrorKind attribute) (cosmolkit.RadicalErrorKind attribute) (cosmolkit.ReactionApplyErrorKind attribute) (cosmolkit.ReactionInitializationErrorKind attribute) (cosmolkit.ReactionModelErrorKind attribute) (cosmolkit.ReactionParseErrorKind attribute) (cosmolkit.ReactionProductErrorKind attribute) (cosmolkit.ReactionRole attribute) (cosmolkit.ReactionRunErrorKind attribute) (cosmolkit.ReactionValidationErrorKind attribute) (cosmolkit.ReactionValidationIssueKind attribute) (cosmolkit.ReactionValidationSeverity attribute) (cosmolkit.ReactionWriteErrorKind attribute) (cosmolkit.RequiredPropertyStringErrorKind attribute) (cosmolkit.ResidueCode attribute) (cosmolkit.ResidueInfoKind attribute) (cosmolkit.ResidueKind attribute) (cosmolkit.ResidueSequenceErrorKind attribute) (cosmolkit.RingDecomposerErrorKind attribute) (cosmolkit.RingFindingErrorKind attribute) (cosmolkit.RotatableBondsOptions attribute) (cosmolkit.SanitizeErrorKind attribute) (cosmolkit.SanitizeStage attribute) (cosmolkit.ScaffoldErrorKind attribute) (cosmolkit.SdfCoordinateMode attribute) (cosmolkit.SdfErrorKind attribute) (cosmolkit.SdfFormat attribute) (cosmolkit.SdfPropertyListTarget attribute) (cosmolkit.SdfReadErrorKind attribute) (cosmolkit.SdfWriteErrorKind attribute) (cosmolkit.SearchMcsErrorKind attribute) (cosmolkit.SelectedBondCopyErrorKind attribute) (cosmolkit.SelectedSubstanceGroupCopyErrorKind attribute) (cosmolkit.SerdeJsonCategory attribute) (cosmolkit.SerialConformerOptimizationErrorKind attribute) (cosmolkit.SerialUffOptimizationErrorKind attribute) (cosmolkit.SingleConformerOptimizationErrorKind attribute) (cosmolkit.SmartsParseErrorKind attribute) (cosmolkit.SmartsTraversalErrorKind attribute) (cosmolkit.SmartsWriteErrorKind attribute) (cosmolkit.SmilesErrorKind attribute) (cosmolkit.SmilesParseErrorKind attribute) (cosmolkit.SmilesStereoErrorKind attribute) (cosmolkit.SmilesWriteErrorKind attribute) (cosmolkit.StereoErrorKind attribute) (cosmolkit.StereoGroupErrorKind attribute) (cosmolkit.StereoGroupKind attribute) (cosmolkit.StereoOrderErrorKind attribute) (cosmolkit.StereoReadErrorKind attribute) (cosmolkit.SubstanceGroupAtomList attribute) (cosmolkit.SubstructMatchErrorKind attribute) (cosmolkit.SvgParseErrorKind attribute) (cosmolkit.TautomerCatalogErrorKind attribute) (cosmolkit.TautomerEnumerationStatus attribute) (cosmolkit.TautomerRunErrorKind attribute) (cosmolkit.TautomerTransformErrorKind attribute) (cosmolkit.TemplateAttachmentOrderErrorKind attribute) (cosmolkit.ThreadCountErrorKind attribute) (cosmolkit.TopologicalFingerprintErrorKind attribute) (cosmolkit.TopologicalTorsionErrorKind attribute) (cosmolkit.TopologicalTorsionPathScoreErrorKind attribute) (cosmolkit.TopologicalTorsionReadErrorKind attribute) (cosmolkit.TopologyEditErrorKind attribute) (cosmolkit.TopologyValidationErrorKind attribute) (cosmolkit.TransformErrorKind attribute) (cosmolkit.UffBondMathErrorKind attribute) (cosmolkit.UffBoundsCauseKind attribute) (cosmolkit.UffBuilderErrorKind attribute) (cosmolkit.UffDefaultTorsionQueryErrorKind attribute) (cosmolkit.UffEvaluationFailureKind attribute) (cosmolkit.UffInversionContributionErrorKind attribute) (cosmolkit.UffInversionIndexArgument attribute) (cosmolkit.UffParamErrorKind attribute) (cosmolkit.UffParameterErrorKind attribute) (cosmolkit.UffParameterQueryErrorKind attribute) (cosmolkit.UffPreparedOptimizationErrorKind attribute) (cosmolkit.UffPreparedValenceField attribute) (cosmolkit.UffThreadCountErrorKind attribute) (cosmolkit.UffTorsionBondQueryErrorKind attribute) (cosmolkit.UffTypingErrorKind attribute) (cosmolkit.UffTypingInput attribute) (cosmolkit.UIntLexicalReadErrorKind attribute) (cosmolkit.UnsignedStreamArrayErrorKind attribute) (cosmolkit.ValenceErrorKind attribute) (cosmolkit.ValenceModel attribute) (cosmolkit.ValencePhase attribute) (cosmolkit.WedgeErrorKind attribute) (cosmolkit.XmlParseErrorKind attribute) (cosmolkit.XyzReadErrorKind attribute) (cosmolkit.XyzWriteErrorKind attribute) namespace (cosmolkit.XmlParseError property) NamespacesLimitReached (cosmolkit.XmlParseErrorKind attribute) NAP (cosmolkit.ResidueCode attribute) Native (cosmolkit.FunctionStatus attribute) NB (cosmolkit.Element attribute) NCO (cosmolkit.ResidueCode attribute) Ncs (cosmolkit.BioMmcifReadStage attribute) ncs (cosmolkit.BioMmcifWriteParams attribute) ncs_oper_identity_id (cosmolkit.BioStructure attribute) ncs_operators (cosmolkit.BioStructure attribute) (cosmolkit.BioStructureParts attribute) ND (cosmolkit.Element attribute) NDG (cosmolkit.ResidueCode attribute) NE (cosmolkit.Element attribute) needs_more (cosmolkit.MmffOptimizeMoleculeConfResult attribute) (cosmolkit.MmffOptimizeMoleculeResult attribute) (cosmolkit.OptimizationOutcome attribute) (cosmolkit.UffConformerResult attribute) (cosmolkit.UffOptimizationResult attribute) NeedsInitialization (cosmolkit.ReactionRunErrorKind attribute) negative (cosmolkit.PropertyIntReadError property) Negative (cosmolkit.PropertyUIntReadErrorKind attribute) (cosmolkit.PropertyULongReadErrorKind attribute) NegativeBase36Value (cosmolkit.BioPdbWriteErrorKind attribute) NegativeFormalCharge (cosmolkit.AtomQueryPredicateKind attribute) (cosmolkit.AtomRangeDataFunctionKind attribute) NegativeImplicitHydrogen (cosmolkit.CipRankErrorKind attribute) NegativeSerial (cosmolkit.BioPdbWriteErrorKind attribute) neighbor (cosmolkit.StereoError property) neighbor_atom (cosmolkit.ValenceError property) neighbor_atom_index (cosmolkit.UffBuilderError property) neighbor_bonds() (cosmolkit.MoleculeBuilder method) neighbor_hydrogens (cosmolkit.ValenceError property) NeighborMatrixAllocationFailed (cosmolkit.UffBuilderErrorKind attribute) NeighborMatrixCellPositionOverflow (cosmolkit.UffBuilderErrorKind attribute) NeighborMatrixIndexOutOfRange (cosmolkit.UffBuilderErrorKind attribute) NeighborMatrixIndexOverflow (cosmolkit.UffBuilderErrorKind attribute) NeighborMatrixStorageOutOfRange (cosmolkit.UffBuilderErrorKind attribute) NEP (cosmolkit.ResidueCode attribute) net_scaffold() (cosmolkit.Molecule method) NetworkDown (cosmolkit.IoErrorKind attribute) NetworkUnreachable (cosmolkit.IoErrorKind attribute) new() (cosmolkit.AlignmentAtomMap static method) (cosmolkit.AlignmentParameters static method) (cosmolkit.AllConformerRmsdParameters static method) (cosmolkit.AtomSpec static method) (cosmolkit.BestAlignmentParameters static method) (cosmolkit.BondSpec static method) (cosmolkit.ConformerAlignmentParameters static method) (cosmolkit.CoordinateRmsdParameters static method) (cosmolkit.EmbedParams static method) (cosmolkit.FingerprintAdditionalOutput static method) (cosmolkit.LegacyTopologicalTorsionParams static method) (cosmolkit.Molecule static method) (cosmolkit.MoleculeBuilder static method) (cosmolkit.MorganBondInvariantsGenerator static method) (cosmolkit.MorganCallParams static method) (cosmolkit.MorganFingerprintGenerator static method) (cosmolkit.ResidueAddress static method) (cosmolkit.ResidueIdentity static method) (cosmolkit.ResidueSourceIds static method) (cosmolkit.SGroupBracket static method) (cosmolkit.SGroupCState static method) (cosmolkit.SparseCountFingerprint static method) (cosmolkit.SparseCountFingerprint32 static method) (cosmolkit.StereoGroup static method) (cosmolkit.SubstanceGroup static method) (cosmolkit.SubstanceGroupId static method) (cosmolkit.TautomerScoreTerm static method) (cosmolkit.TopologicalTorsionFingerprintGenerator static method) next() (cosmolkit.StereoisomerIterator method) next_batch() (cosmolkit.SdfBatchIterator method) (cosmolkit.SdfReaderBatchIterator method) next_record() (cosmolkit.SdfRecordStream method) NGA (cosmolkit.ResidueCode attribute) NH (cosmolkit.Element attribute) NH2 (cosmolkit.ResidueCode attribute) NH4 (cosmolkit.ResidueCode attribute) NHE (cosmolkit.ResidueCode attribute) NI (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) NLE (cosmolkit.ResidueCode attribute) NO (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) NO3 (cosmolkit.ResidueCode attribute) No3dConformer (cosmolkit.MatrixErrorKind attribute) (cosmolkit.TransformErrorKind attribute) NO_BOND_ORDER (cosmolkit.PdbWriteFlags attribute) no_implicit (cosmolkit.Atom attribute) (cosmolkit.MoleculeAtom attribute) (cosmolkit.QueryAtom attribute) NoAtomsProvided (cosmolkit.FragmentWriteInputErrorKind attribute) NoCanonicalTautomer (cosmolkit.TautomerRunErrorKind attribute) NoCommonAtoms (cosmolkit.Coordinate2DLayoutErrorKind attribute) NoConformers (cosmolkit.AlignmentErrorKind attribute) node (cosmolkit.CipLabelerError property) (cosmolkit.RingDecomposerError property) node_count (cosmolkit.RingDecomposerError property) NodeOutOfRange (cosmolkit.RingDecomposerErrorKind attribute) NodesLimitReached (cosmolkit.XmlParseErrorKind attribute) NoDistanceMatrix (cosmolkit.ForceFieldKernelErrorKind attribute) NoError (cosmolkit.JsonErrorKind attribute) NoHydrogen (cosmolkit.BioCalcFlag attribute) NoModelAfterDefault (cosmolkit.PdbStructureFinalizationErrorKind attribute) NoModelsAfterSourceDefault (cosmolkit.PdbCisPepRecordErrorKind attribute) non_ascii (cosmolkit.PdbHelixError attribute) (cosmolkit.PdbModResError attribute) (cosmolkit.PdbSheetError attribute) non_ascii_line (cosmolkit.BioStructureSourceState attribute) non_bonded_threshold (cosmolkit.MmffConformerOptimizationParams attribute) (cosmolkit.MmffEvaluationParams attribute) (cosmolkit.MmffForceFieldParams attribute) (cosmolkit.MmffOptimizationParams attribute) NON_SSS_BITS (cosmolkit.AvalonFingerprintFlags attribute) NonAminoAcidResidue (cosmolkit.ProteinProjectionErrorKind attribute) Nonbonded (cosmolkit.ForceFieldConstructionErrorKind attribute) NonbondedAssemblyError NonbondedAssemblyErrorKind (class in cosmolkit) NonbondedFragmentMappingError NonbondedFragmentMappingErrorKind (class in cosmolkit) NonContiguousSpan (cosmolkit.BioStructureErrorKind attribute) NONE (cosmolkit.BondDirection attribute) (cosmolkit.CxSmilesFields attribute) (cosmolkit.PdbReadFlags attribute) (cosmolkit.PdbWriteFlags attribute) (cosmolkit.PotentialStereoDescriptor attribute) (cosmolkit.SanitizeOperations attribute) None_ (cosmolkit.BondDirection attribute) (cosmolkit.BondStereo attribute) (cosmolkit.PotentialStereoDescriptor attribute) (cosmolkit.SanitizeStage attribute) NonElementAtomicNumber (cosmolkit.QueryAtomConversionErrorKind attribute) NonElementAtomIdentity (cosmolkit.QueryStateErrorKind attribute) NonElementIdentity (cosmolkit.Coordinate2DTemplateErrorKind attribute) NonFinite (cosmolkit.CoordinateInputErrorKind attribute) NonFiniteCoordinate (cosmolkit.CoordinateValidationErrorKind attribute) (cosmolkit.MolecularForceFieldErrorKind attribute) NonFinitePoint (cosmolkit.TransformErrorKind attribute) NonFiniteTransform (cosmolkit.TransformErrorKind attribute) NonFiniteWeight (cosmolkit.TransformErrorKind attribute) NonHydrogenDegree (cosmolkit.AtomQueryPredicateKind attribute) (cosmolkit.AtomRangeDataFunctionKind attribute) NonHydrogenDegreeGreaterEqual (cosmolkit.AtomQueryPredicateKind attribute) NonHydrogenDegreeLessEqual (cosmolkit.AtomQueryPredicateKind attribute) NonIntegerBondOrder (cosmolkit.CipLabelerErrorKind attribute) NonPolymer (cosmolkit.EntityKind attribute) NonpolymerSubchainCounterOutsideSourceIntRange (cosmolkit.PdbModelTransitionErrorKind attribute) NonPositiveWeight (cosmolkit.AlignmentErrorKind attribute) NonSingleBond (cosmolkit.WedgeErrorKind attribute) NonStrict (cosmolkit.RotatableBondsOptions attribute) NonTetrahedralLigandOverflow (cosmolkit.Coordinate2DLayoutErrorKind attribute) NonTetrahedralNoLigand (cosmolkit.Coordinate2DLayoutErrorKind attribute) NonXmlChar (cosmolkit.XmlParseErrorKind attribute) nonzero_elements (cosmolkit.SparseCountFingerprint attribute) (cosmolkit.SparseCountFingerprint32 attribute) NonZeroZ (cosmolkit.CoordinateInputErrorKind attribute) NoPoints (cosmolkit.ForceFieldKernelErrorKind attribute) NoRecord (cosmolkit.MolecularIoErrorKind attribute) normalization (cosmolkit.AtropisomerError property) Normalization (cosmolkit.AtropisomerErrorKind attribute) NoRootNode (cosmolkit.XmlParseErrorKind attribute) NoSelectedAtoms (cosmolkit.TransformErrorKind attribute) NoSequenceRuleProvided (cosmolkit.CipLabelerErrorKind attribute) NoStructuralModels (cosmolkit.MmcifConnectionErrorKind attribute) NoSubstructureMatch (cosmolkit.AlignmentErrorKind attribute) not_converged_with_energy() (cosmolkit.OptimizationOutcome static method) NotADirectory (cosmolkit.IoErrorKind attribute) NotAnUtf8Str (cosmolkit.SvgParseErrorKind attribute) NotApplicable (cosmolkit.BioAssemblySpecialKind attribute) (cosmolkit.ParityPolicy attribute) NotChemComp (cosmolkit.ChemCompModelErrorKind attribute) NotConnected (cosmolkit.IoErrorKind attribute) NotConverged (cosmolkit.OptimizationStatus attribute) NotDoubleBond (cosmolkit.DoubleBondStereoErrorKind attribute) NotEnoughEmbeddedNeighbors (cosmolkit.Coordinate2DLayoutErrorKind attribute) NotFound (cosmolkit.IoErrorKind attribute) NotInitialized (cosmolkit.ForceFieldKernelErrorKind attribute) NotKekulizable (cosmolkit.KekulizeErrorKind attribute) NotRingSystem (cosmolkit.Coordinate2DTemplateErrorKind attribute) NotSeekable (cosmolkit.IoErrorKind attribute) NotSet (cosmolkit.BioCalcFlag attribute) NP (cosmolkit.Element attribute) NRQ (cosmolkit.ResidueCode attribute) Null (cosmolkit.MmjsonUnexpectedType attribute) NullBondAtom (cosmolkit.TopologyEditErrorKind attribute) num_3d_conformers (cosmolkit.Molecule attribute) num_agent_templates (cosmolkit.Reaction attribute) num_aliphatic_carbocycles() (cosmolkit.Molecule method) num_aliphatic_heterocycles() (cosmolkit.Molecule method) num_aliphatic_rings() (cosmolkit.Molecule method) num_amide_bonds() (cosmolkit.Molecule method) num_aromatic_carbocycles() (cosmolkit.Molecule method) num_aromatic_heterocycles() (cosmolkit.Molecule method) num_aromatic_rings() (cosmolkit.Molecule method) num_atom_pair_fingerprint_bits() (cosmolkit.AtomPairsParameters static method) num_atom_stereo_centers() (cosmolkit.Molecule method) num_atoms (cosmolkit.BioResidue attribute) (cosmolkit.BioStructure attribute) (cosmolkit.CompiledQuery attribute) (cosmolkit.Molecule attribute) (cosmolkit.Protein attribute) (cosmolkit.QueryGraph attribute) (cosmolkit.TautomerMoleculeView attribute) num_bits_per_feature (cosmolkit.TopologicalFingerprintParams attribute) num_bonds (cosmolkit.CompiledQuery attribute) (cosmolkit.Molecule attribute) (cosmolkit.QueryGraph attribute) (cosmolkit.TautomerMoleculeView attribute) num_branch_bits() (cosmolkit.AtomPairsParameters static method) num_bridgehead_atoms() (cosmolkit.Molecule method) num_chains (cosmolkit.BioModel attribute) (cosmolkit.BioStructure attribute) (cosmolkit.Protein attribute) num_chiral_bits() (cosmolkit.AtomPairsParameters static method) num_entities (cosmolkit.BioStructure attribute) num_errors (cosmolkit.ReactionValidationReport attribute) num_hba() (cosmolkit.Molecule method) num_hbd() (cosmolkit.Molecule method) num_heavy_atoms() (cosmolkit.Molecule method) num_heteroatoms() (cosmolkit.Molecule method) num_heterocycles() (cosmolkit.Molecule method) num_id (cosmolkit.BioTlsGroup attribute) num_models (cosmolkit.BioStructure attribute) (cosmolkit.Protein attribute) num_path_bits() (cosmolkit.AtomPairsParameters static method) num_pi_bits() (cosmolkit.AtomPairsParameters static method) num_points (cosmolkit.ForceFieldKernelError property) num_product_templates (cosmolkit.Reaction attribute) num_reactant_templates (cosmolkit.Reaction attribute) num_residues (cosmolkit.BioChain attribute) (cosmolkit.BioStructure attribute) (cosmolkit.Protein attribute) num_rings (cosmolkit.RingSearchResult attribute) num_rings() (cosmolkit.Molecule method) num_rotatable_bonds() (cosmolkit.Molecule method) num_rotatable_bonds_with_params() (cosmolkit.Molecule method) num_saturated_carbocycles() (cosmolkit.Molecule method) num_saturated_heterocycles() (cosmolkit.Molecule method) num_saturated_rings() (cosmolkit.Molecule method) num_spiro_atoms() (cosmolkit.Molecule method) num_threads (cosmolkit.AllConformerRmsdParameters attribute) (cosmolkit.BestAlignmentParameters attribute) (cosmolkit.EmbedParams attribute) (cosmolkit.MmffConformerOptimizationParams attribute) (cosmolkit.SubstructMatchParams attribute) (cosmolkit.UffConformerOptimizationParams attribute) num_transforms (cosmolkit.TautomerProgress attribute) num_type_bits() (cosmolkit.AtomPairsParameters static method) num_unspecified_atom_stereo_centers() (cosmolkit.Molecule method) num_warnings (cosmolkit.ReactionValidationReport attribute) num_zero_fail (cosmolkit.EmbedParams attribute) NumAliphaticHeteroatomNeighbors (cosmolkit.AtomQueryPredicateKind attribute) (cosmolkit.AtomRangeDataFunctionKind attribute) NumAtomRings (cosmolkit.AtomQueryPredicateKind attribute) (cosmolkit.AtomRangeDataFunctionKind attribute) number (cosmolkit.BioSiftsUnpResidue attribute) Number (cosmolkit.ChemCompAtomErrorKind attribute) number (cosmolkit.PdbModelTransitionError property) number_of_crystals (cosmolkit.BioExperimentInfo attribute) numbered_ter (cosmolkit.BioPdbWriteParams attribute) NumberOutsideU16 (cosmolkit.MmcifSiftsUnpErrorKind attribute) Numeric (cosmolkit.CxQueryLoweringErrorKind attribute) numeric (cosmolkit.GenerationError property) Numeric (cosmolkit.GenerationErrorKind attribute) NumericalPrecondition (cosmolkit.AlignmentErrorKind attribute) NumericIdOutsideSourceDefinedRange (cosmolkit.MmcifTlsInfoErrorKind attribute) NumericPropertyRead (cosmolkit.DoubleBondStereoErrorKind attribute) NumHeteroatomNeighbors (cosmolkit.AtomQueryPredicateKind attribute) (cosmolkit.AtomRangeDataFunctionKind attribute) NumRadicalElectrons (cosmolkit.AtomQueryPredicateKind attribute) NumRingBonds (cosmolkit.BondQueryPredicateKind attribute) NumRingBondsGreaterEqual (cosmolkit.BondQueryPredicateKind attribute) NumRingBondsLessEqual (cosmolkit.BondQueryPredicateKind attribute) O O (cosmolkit.Element attribute) OAS (cosmolkit.ResidueCode attribute) Object (cosmolkit.MmjsonUnexpectedType attribute) ObservationIo (cosmolkit.ThreadCountErrorKind attribute) occupancy (cosmolkit.BioAtom attribute) (cosmolkit.BioAtomRow attribute) OCS (cosmolkit.ResidueCode attribute) Octahedral (cosmolkit.ChiralTag attribute) offset (cosmolkit.CxParseError property) (cosmolkit.PdbModelTransitionError property) (cosmolkit.PdbRemark350Error attribute) (cosmolkit.PdbRemarkMetadataError attribute) (cosmolkit.SmilesParseError property) OffsetOverflow (cosmolkit.ReactionParseErrorKind attribute) OG (cosmolkit.Element attribute) ok (cosmolkit.EmbedMoleculeResult attribute) old_bond_count (cosmolkit.StereoOrderError property) oligomeric_count (cosmolkit.BioAssembly attribute) oligomeric_details (cosmolkit.BioAssembly attribute) OMC (cosmolkit.ResidueCode attribute) OMG (cosmolkit.ResidueCode attribute) OMIT_SINGLE_CONECT (cosmolkit.PdbWriteFlags attribute) OMU (cosmolkit.ResidueCode attribute) OMY (cosmolkit.ResidueCode attribute) OMZ (cosmolkit.ResidueCode attribute) on_bits (cosmolkit.Fingerprint attribute) (cosmolkit.SparseBitFingerprint attribute) one_letter_code (cosmolkit.ProteinResidueRef attribute) (cosmolkit.ResidueInfo attribute) ONEANDAHALF (cosmolkit.BondOrder attribute) OneAndHalf (cosmolkit.BondOrder attribute) only_altloc (cosmolkit.BioCisPep attribute) only_heavy_atoms_for_rms (cosmolkit.EmbedParams attribute) only_nonzero_invariants (cosmolkit.MorganFingerprintParams attribute) (cosmolkit.MorganGeneratorParams attribute) (cosmolkit.MorganSettings attribute) only_on_atoms (cosmolkit.AddHsParams attribute) only_shortest_paths (cosmolkit.TopologicalTorsionFingerprintParams attribute) (cosmolkit.TopologicalTorsionGeneratorParams attribute) (cosmolkit.TopologicalTorsionSettings attribute) only_stereo_groups (cosmolkit.StereoisomerOptions attribute) only_unassigned (cosmolkit.StereoisomerOptions attribute) OnlyOnAtomOutOfRange (cosmolkit.HydrogenErrorKind attribute) oop (cosmolkit.MmffParamError property) Oop (cosmolkit.MmffParamErrorKind attribute) (cosmolkit.MmffParamTable attribute) OopAddressOutsideDefinedSource (cosmolkit.ForceFieldKernelErrorKind attribute) OopParametersMissing (cosmolkit.ForceFieldKernelErrorKind attribute) open() (cosmolkit.SdfDataset static method) (cosmolkit.SdfReader static method) (cosmolkit.SdfRecordStream static method) open_with_params() (cosmolkit.SdfDataset static method) (cosmolkit.SdfReader static method) (cosmolkit.SdfRecordStream static method) Operation (cosmolkit.AtomPropertyReadErrorKind attribute) operation (cosmolkit.BatchError property) (cosmolkit.BioStructureError property) (cosmolkit.ChemistryProblem attribute) (cosmolkit.HydrogenError property) (cosmolkit.InchiError property) (cosmolkit.OperationError property) (cosmolkit.OperationInvariantEntry attribute) (cosmolkit.ParityMatrixEntry attribute) (cosmolkit.SupportMatrixEntry attribute) (cosmolkit.WedgeError property) operation_invariant() (in module cosmolkit) operation_invariant_matrix() (in module cosmolkit) operation_parity() (in module cosmolkit) operation_spec() (in module cosmolkit) operation_specs() (in module cosmolkit) OperationCipStatePolicy (class in cosmolkit) OperationContract (cosmolkit.OperationErrorKind attribute) OperationDerivedState (class in cosmolkit) OperationError OperationErrorKind (class in cosmolkit) OperationExpr (cosmolkit.MmcifAssemblyErrorKind attribute) OperationInvariantEntry (class in cosmolkit) OperationMappingRequirement (class in cosmolkit) operations (cosmolkit.SanitizeParams attribute) OperationSemanticPreconditions (class in cosmolkit) operator_type (cosmolkit.BioAssemblyOperator attribute) operators (cosmolkit.BioAssemblyGenerator attribute) optics (cosmolkit.BioDiffractionInfo attribute) Optimization (cosmolkit.SerialConformerOptimizationErrorKind attribute) (cosmolkit.SerialUffOptimizationErrorKind attribute) (cosmolkit.SingleConformerOptimizationErrorKind attribute) (cosmolkit.UffOptimizationErrorKind attribute) OptimizationOutcome (class in cosmolkit) OptimizationStageError OptimizationStageErrorKind (class in cosmolkit) OptimizationStatus (class in cosmolkit) optimizer_force_tol (cosmolkit.EmbedParams attribute) OptimizerBadDirection (cosmolkit.ForceFieldKernelErrorKind attribute) OptimizerBadTolerance (cosmolkit.ForceFieldKernelErrorKind attribute) option (cosmolkit.MaccsFingerprintError property) options (cosmolkit.InchiWriteParams attribute) Or (cosmolkit.StereoGroupKind attribute) OrAboveAndBelowAnd (cosmolkit.SmartsWriteErrorKind attribute) order (cosmolkit.Bond attribute) Order (cosmolkit.BondQueryPredicateKind attribute) order (cosmolkit.CipLabelerError property) (cosmolkit.CipRankError property) (cosmolkit.DoubleBondStereoError property) (cosmolkit.ForceFieldKernelError property) (cosmolkit.MatrixError property) Order (cosmolkit.McsBondComparator attribute) order (cosmolkit.PotentialStereoError property) (cosmolkit.ValenceError property) order_code (cosmolkit.Bond attribute) order_name (cosmolkit.Bond attribute) OrderedFragmentBuildError OrderedFragmentBuildErrorKind (class in cosmolkit) OrderExact (cosmolkit.McsBondComparator attribute) OrderIn (cosmolkit.BondQueryPredicateKind attribute) origin (cosmolkit.BioTlsGroup attribute) original_explicit_hydrogens (cosmolkit.AdjustHsError property) original_implicit_valence (cosmolkit.AdjustHsError property) Origx (cosmolkit.BioMmcifReadStage attribute) origx (cosmolkit.BioMmcifWriteParams attribute) (cosmolkit.BioStructure attribute) (cosmolkit.BioStructureSourceState attribute) ORN (cosmolkit.ResidueCode attribute) orthogonal (cosmolkit.BioCrystalInfo attribute) OS (cosmolkit.Element attribute) OTE (cosmolkit.ResidueCode attribute) OTHER (cosmolkit.BondOrder attribute) Other (cosmolkit.BondOrder attribute) (cosmolkit.ChiralTag attribute) OTHER (cosmolkit.Hybridization attribute) Other (cosmolkit.Hybridization attribute) (cosmolkit.IoErrorKind attribute) (cosmolkit.PolymerKind attribute) other (cosmolkit.RingStereoRelation attribute) outcome (cosmolkit.MmffOptimizeMoleculeConfResult attribute) (cosmolkit.MmffOptimizeMoleculeResult attribute) (cosmolkit.UffConformerResult attribute) (cosmolkit.UffOptimizationResult attribute) outer_electrons (cosmolkit.ElementInfo attribute) OutOfMemory (cosmolkit.IoErrorKind attribute) (cosmolkit.JsonErrorKind attribute) OutOfRange (cosmolkit.BondEndPointsParseErrorKind attribute) (cosmolkit.CifReadErrorKind attribute) (cosmolkit.MappingValidationErrorKind attribute) output_atoms (cosmolkit.AromaticityError property) output_bonds (cosmolkit.AromaticityError property) OutputAllocation (cosmolkit.TopologicalTorsionErrorKind attribute) OutputMismatch (cosmolkit.OperationErrorKind attribute) OutputNotRequested (cosmolkit.TopologicalFingerprintErrorKind attribute) OutputUtf8 (cosmolkit.MolecularIoErrorKind attribute) Overflow (cosmolkit.DoubleLexicalReadErrorKind attribute) (cosmolkit.UIntLexicalReadErrorKind attribute) P P (cosmolkit.CipDescriptor attribute) p (cosmolkit.CipDescriptor attribute) P (cosmolkit.Element attribute) P33 (cosmolkit.ResidueCode attribute) P4C (cosmolkit.ResidueCode attribute) PA (cosmolkit.Element attribute) PAA (cosmolkit.ResidueInfoKind attribute) PackedAngleBoundsOrder (cosmolkit.ForceFieldKernelErrorKind attribute) PackedCode (cosmolkit.TopologicalTorsionPathScoreErrorKind attribute) PairBuilder (cosmolkit.NonbondedAssemblyErrorKind attribute) Panic (cosmolkit.FingerprintWorkerErrorKind attribute) parallel_jobs (cosmolkit.MoleculeBatch attribute) Parameter (cosmolkit.MolecularIoErrorKind attribute) parameter (cosmolkit.UffBoundsCause attribute) Parameter (cosmolkit.UffBoundsCauseKind attribute) Parameterization (cosmolkit.MolecularForceFieldErrorKind attribute) Parameters (cosmolkit.UffParameterQueryErrorKind attribute) ParameterTable (cosmolkit.AutomaticForceFieldConstructionErrorKind attribute) (cosmolkit.UffParameterErrorKind attribute) params (cosmolkit.EmbedMoleculeResult attribute) (cosmolkit.EmbedMultipleConfsResult attribute) (cosmolkit.MmffMolPropertiesError property) Params (cosmolkit.MmffMolPropertiesErrorKind attribute) params (cosmolkit.MorganSettings attribute) (cosmolkit.SdfReader attribute) (cosmolkit.TopologicalTorsionSettings attribute) (cosmolkit.UffBuilderError property) ParamsLengthMismatch (cosmolkit.UffBuilderErrorKind attribute) parent (cosmolkit.QueryGraphError property) (cosmolkit.TopologyValidationError property) parent_comp_id (cosmolkit.BioModRes attribute) parent_standard_code (cosmolkit.ResidueInfo attribute) ParentAtoms (cosmolkit.SubstanceGroupAtomList attribute) ParentMismatch (cosmolkit.BioStructureErrorKind attribute) parity (cosmolkit.MoleculeOpSpec attribute) parity_matrix() (in module cosmolkit) ParityMatrixEntry (class in cosmolkit) ParityPolicy (class in cosmolkit) ParityVectorsMustHaveSize4 (cosmolkit.CipLabelerErrorKind attribute) Parse (cosmolkit.FingerprintJsonErrorKind attribute) (cosmolkit.MmjsonReadErrorKind attribute) (cosmolkit.Mol2ReadErrorKind attribute) (cosmolkit.SdfReadErrorKind attribute) (cosmolkit.SmartsParseErrorKind attribute) (cosmolkit.SmilesErrorKind attribute) (cosmolkit.UffDefaultTorsionQueryErrorKind attribute) (cosmolkit.UffTorsionBondQueryErrorKind attribute) parse_name (cosmolkit.SmartsParseParams attribute) (cosmolkit.SmilesParseParams attribute) parse_smarts() (in module cosmolkit) parse_smarts_with_params() (in module cosmolkit) parse_smirks() (in module cosmolkit) parse_smirks_with_params() (in module cosmolkit) parsed_count (cosmolkit.MmcifAtomSiteRowOutOfBounds property) ParseFloat (cosmolkit.UffParamErrorKind attribute) ParseFloatError ParserAtropisomer (cosmolkit.SmilesParseErrorKind attribute) ParserCarrier (cosmolkit.SmartsParseErrorKind attribute) (cosmolkit.SmilesParseErrorKind attribute) ParserCarrierError ParserCarrierErrorKind (class in cosmolkit) ParserCleanup (cosmolkit.ReactionParseErrorKind attribute) ParserRemoveHydrogens (cosmolkit.SmilesParseErrorKind attribute) ParserSanitize (cosmolkit.SmilesParseErrorKind attribute) ParserStereo (cosmolkit.SmilesParseErrorKind attribute) ParserStereoOrderError ParserStereoOrderErrorKind (class in cosmolkit) parsing_failed (cosmolkit.SvgParseError property) ParsingFailed (cosmolkit.SvgParseErrorKind attribute) partial_charge (cosmolkit.MmffAtomProperties attribute) partial_charge() (cosmolkit.MmffProperties method) partner (cosmolkit.MmcifCisPepError property) (cosmolkit.MmcifConnectionError property) (cosmolkit.PdbCisPepRecordError attribute) (cosmolkit.PdbLinkRecordError attribute) (cosmolkit.PdbSsbondRecordError attribute) (cosmolkit.PdbSsbondResolutionError property) partner1 (cosmolkit.BioConnection attribute) partner2 (cosmolkit.BioConnection attribute) partner_c (cosmolkit.BioCisPep attribute) partner_n (cosmolkit.BioCisPep attribute) path (cosmolkit.BioMmcifWriteError property) (cosmolkit.BioPdbWriteError property) (cosmolkit.BioReadError property) (cosmolkit.Coordinate2DTemplateError property) Path (cosmolkit.DescriptorErrorKind attribute) path (cosmolkit.DrawingWriteError property) (cosmolkit.MolecularIoError property) (cosmolkit.SdfDataset attribute) (cosmolkit.SdfReader attribute) (cosmolkit.TautomerCatalogError property) Path (cosmolkit.TopologicalTorsionErrorKind attribute) PathError PathErrorKind (class in cosmolkit) Paths (cosmolkit.LayeredFingerprintErrorKind attribute) (cosmolkit.MaccsFingerprintErrorKind attribute) (cosmolkit.TopologicalFingerprintErrorKind attribute) PatternFingerprintError PatternFingerprintErrorKind (class in cosmolkit) PatternFingerprintParams (class in cosmolkit) PB (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) Pbci (cosmolkit.MmffParamTable attribute) PCA (cosmolkit.ResidueCode attribute) PD (cosmolkit.Element attribute) Pdb (cosmolkit.BioCoordinateFormat attribute) (cosmolkit.BioReadErrorKind attribute) (cosmolkit.ProteinReadErrorKind attribute) pdb_helix_class (cosmolkit.BioHelix attribute) PdbAtomFieldError (class in cosmolkit) PdbAtomFieldErrorKind (class in cosmolkit) PdbChargeError (class in cosmolkit) PdbCisPepRecordError (class in cosmolkit) PdbCisPepRecordErrorKind (class in cosmolkit) PdbConectError (class in cosmolkit) PdbConectErrorKind (class in cosmolkit) PdbConnectionFinalizationError (class in cosmolkit) PdbConnectionFinalizationErrorKind (class in cosmolkit) PdbCrystalError (class in cosmolkit) PdbCrystalErrorKind (class in cosmolkit) PdbDbRefError (class in cosmolkit) PdbDbRefErrorKind (class in cosmolkit) PdbHeaderError PdbHeaderErrorKind (class in cosmolkit) PdbHelixError (class in cosmolkit) PdbHelixErrorKind (class in cosmolkit) PdbInputFormatError PdbInputFormatErrorKind (class in cosmolkit) PdbLinkNameCounter (class in cosmolkit) PdbLinkRecordError (class in cosmolkit) PdbLinkRecordErrorKind (class in cosmolkit) PdbModelTransitionError PdbModelTransitionErrorKind (class in cosmolkit) PdbModResError (class in cosmolkit) PdbModResErrorKind (class in cosmolkit) PdbMtrixError (class in cosmolkit) PdbMtrixErrorKind (class in cosmolkit) PdbPostprocessError PdbPostprocessErrorKind (class in cosmolkit) PdbRead (cosmolkit.MolecularIoErrorKind attribute) PdbReaderCause PdbReaderCauseKind (class in cosmolkit) PdbReadFlags (class in cosmolkit) PdbRemark200Error (class in cosmolkit) PdbRemark200ErrorKind (class in cosmolkit) PdbRemark350Error (class in cosmolkit) PdbRemark350ErrorKind (class in cosmolkit) PdbRemark3Error (class in cosmolkit) PdbRemark3ErrorKind (class in cosmolkit) PdbRemarkError PdbRemarkErrorKind (class in cosmolkit) PdbRemarkFinalizationError (class in cosmolkit) PdbRemarkFinalizationErrorKind (class in cosmolkit) PdbRemarkMetadataError (class in cosmolkit) PdbRemarkMetadataErrorKind (class in cosmolkit) PdbResidueKeyError PdbResidueKeyErrorKind (class in cosmolkit) PdbSeqId (class in cosmolkit) PdbSheetError (class in cosmolkit) PdbSheetErrorKind (class in cosmolkit) PdbSsbondRecordError (class in cosmolkit) PdbSsbondRecordErrorKind (class in cosmolkit) PdbSsbondResolutionError PdbStructureFinalizationError (class in cosmolkit) PdbStructureFinalizationErrorKind (class in cosmolkit) PdbWrite (cosmolkit.MolecularIoErrorKind attribute) PdbWriteError PdbWriteErrorKind (class in cosmolkit) PdbWriteFlags (class in cosmolkit) PdbWriteParams (class in cosmolkit) PDO (cosmolkit.ResidueCode attribute) PE4 (cosmolkit.ResidueCode attribute) PE7 (cosmolkit.ResidueCode attribute) PE8 (cosmolkit.ResidueCode attribute) PEG (cosmolkit.ResidueCode attribute) PeptideD (cosmolkit.PolymerKind attribute) PeptideL (cosmolkit.PolymerKind attribute) perceive_stereochemistry() (cosmolkit.Molecule method) period (cosmolkit.ElementInfo attribute) periodic_table (cosmolkit.CipLabelerError property) (cosmolkit.PathError property) (cosmolkit.SubstructMatchError property) PeriodicTable (cosmolkit.CipLabelerErrorKind attribute) (cosmolkit.MorganErrorKind attribute) (cosmolkit.PathErrorKind attribute) (cosmolkit.SubstructMatchErrorKind attribute) PeriodicTableError PeriodicTableErrorKind (class in cosmolkit) PeriodicTableLookup (cosmolkit.RadicalErrorKind attribute) (cosmolkit.ValenceErrorKind attribute) PermissionDenied (cosmolkit.IoErrorKind attribute) permutation (cosmolkit.PotentialStereoError property) (cosmolkit.PotentialStereoInfo attribute) PermutationAtomOutOfRange (cosmolkit.TopologyEditErrorKind attribute) PermutationDuplicateAtom (cosmolkit.TopologyEditErrorKind attribute) PermutationLength (cosmolkit.StereoOrderErrorKind attribute) (cosmolkit.TopologyEditErrorKind attribute) permute_degree_four (cosmolkit.Coordinate2DParams attribute) PEU (cosmolkit.ResidueCode attribute) PG4 (cosmolkit.ResidueCode attribute) PG5 (cosmolkit.ResidueCode attribute) PG6 (cosmolkit.ResidueCode attribute) PGE (cosmolkit.ResidueCode attribute) PGO (cosmolkit.ResidueCode attribute) PGQ (cosmolkit.ResidueCode attribute) PGR (cosmolkit.ResidueCode attribute) ph (cosmolkit.BioExperimentalCrystalInfo attribute) ph_range (cosmolkit.BioExperimentalCrystalInfo attribute) phase (cosmolkit.ValenceError property) Phasing (cosmolkit.BioSoftwareClassification attribute) PHD (cosmolkit.ResidueCode attribute) PHE (cosmolkit.ResidueCode attribute) PHI (cosmolkit.ResidueCode attribute) phi() (cosmolkit.Molecule method) PHL (cosmolkit.ResidueCode attribute) physical_bonds (cosmolkit.ValenceError property) pi_electrons (cosmolkit.AtomCodeExplanation attribute) PickleError PickleErrorKind (class in cosmolkit) PiElectronExplicitValenceCacheNotInitialized (cosmolkit.ValenceErrorKind attribute) PiElectronInvariant (cosmolkit.ValenceErrorKind attribute) PIG (cosmolkit.ResidueCode attribute) PIN (cosmolkit.ResidueCode attribute) PixmapAllocation (cosmolkit.DrawingErrorKind attribute) Placement (cosmolkit.AttachmentExpansionErrorKind attribute) platform (cosmolkit.ThreadCountError property) PLP (cosmolkit.ResidueCode attribute) PM (cosmolkit.Element attribute) Pna (cosmolkit.PolymerKind attribute) PngEncode (cosmolkit.DrawingErrorKind attribute) PO (cosmolkit.Element attribute) PO4 (cosmolkit.ResidueCode attribute) points (cosmolkit.SGroupBracket attribute) PoisonError POL (cosmolkit.ResidueCode attribute) policy (cosmolkit.OperationError property) POLYMER (cosmolkit.CxSmilesFields attribute) Polymer (cosmolkit.EntityKind attribute) polymer_kind (cosmolkit.BioEntityRow attribute) PolymerKind (class in cosmolkit) pos (cosmolkit.BioSelectionParseError property) position (cosmolkit.BioAtom attribute) (cosmolkit.HydrogenError property) (cosmolkit.MatrixError property) (cosmolkit.PathError property) (cosmolkit.ProteinAtomRef attribute) (cosmolkit.QueryGraphError property) (cosmolkit.QueryStateError property) (cosmolkit.SmartsParseError property) (cosmolkit.StereoOrderError property) (cosmolkit.SubstructMatchError property) (cosmolkit.TemplateAttachmentOrderError property) (cosmolkit.TopologyEditError property) (cosmolkit.TopologyValidationError property) (cosmolkit.UffBuilderError property) (cosmolkit.UIntLexicalReadError property) (cosmolkit.XmlParseError property) position() (cosmolkit.MolecularForceField method) position_count (cosmolkit.ForceFieldKernelError property) PositionCountMismatch (cosmolkit.ForceFieldKernelErrorKind attribute) positions (cosmolkit.BioCoordinateBlock attribute) (cosmolkit.MolecularForceField attribute) Post (cosmolkit.SdfErrorKind attribute) Postcondition (cosmolkit.AtomCodeErrorKind attribute) PostconditionValenceMismatch (cosmolkit.KekulizeErrorKind attribute) potential_stereo (cosmolkit.EnumerationError property) (cosmolkit.LegacyStereoError property) (cosmolkit.OperationError property) (cosmolkit.WedgeError property) potential_stereo() (cosmolkit.Molecule method) potential_stereo_with_params() (cosmolkit.Molecule method) PotentialStereo (cosmolkit.EnumerationErrorKind attribute) (cosmolkit.LegacyStereoErrorKind attribute) (cosmolkit.OperationErrorKind attribute) (cosmolkit.StereoReadErrorKind attribute) (cosmolkit.WedgeErrorKind attribute) PotentialStereoCenter (class in cosmolkit) PotentialStereoDescriptor (class in cosmolkit) PotentialStereoError PotentialStereoErrorKind (class in cosmolkit) PotentialStereoInfo (class in cosmolkit) PotentialStereoParams (class in cosmolkit) PotentialStereoResult (class in cosmolkit) PotentialStereoSpecified (class in cosmolkit) PotentialStereoType (class in cosmolkit) PR (cosmolkit.Element attribute) precision (cosmolkit.MolBlockWriteParams attribute) (cosmolkit.XyzWriteParams attribute) Precondition (cosmolkit.AtomCodeErrorKind attribute) PreconditionViolation (cosmolkit.FingerprintErrorKind attribute) predicate (cosmolkit.SmartsWriteError property) prefer_pairs (cosmolkit.BioMmcifWriteParams attribute) prefix (cosmolkit.XmlParseError property) Preparation (cosmolkit.AtomPairErrorKind attribute) (cosmolkit.AtomPairReadErrorKind attribute) (cosmolkit.MolecularForceFieldErrorKind attribute) (cosmolkit.MorganReadErrorKind attribute) (cosmolkit.TopologicalTorsionErrorKind attribute) (cosmolkit.TopologicalTorsionReadErrorKind attribute) preparation (cosmolkit.UffEvaluationFailure attribute) Preparation (cosmolkit.UffEvaluationFailureKind attribute) (cosmolkit.UffParameterErrorKind attribute) (cosmolkit.UffPreparedOptimizationErrorKind attribute) prepared_target (cosmolkit.CrystalffTorsionPreferencesError property) PreparedRingLength (cosmolkit.CanonicalRankErrorKind attribute) PreparedStateLength (cosmolkit.UffTypingErrorKind attribute) PreparedTarget (cosmolkit.CrystalffTorsionPreferencesErrorKind attribute) PreparedValenceInvalid (cosmolkit.CanonicalRankErrorKind attribute) PreparedValenceLength (cosmolkit.CanonicalRankErrorKind attribute) Preserve (cosmolkit.SdfCoordinateMode attribute) preserve_serial (cosmolkit.BioPdbWriteParams attribute) PRO (cosmolkit.ResidueCode attribute) probe (cosmolkit.StereoOrderError property) probe_atom (cosmolkit.AlignmentAtomMap attribute) probe_conformer_id (cosmolkit.AlignmentParameters attribute) (cosmolkit.BestAlignmentParameters attribute) (cosmolkit.ConformerRmsd attribute) (cosmolkit.CoordinateRmsdParameters attribute) probe_count (cosmolkit.ParserStereoOrderError property) probe_index (cosmolkit.ParserStereoOrderError property) ProbeAtomOutOfRange (cosmolkit.AlignmentErrorKind attribute) ProbeLengthMismatch (cosmolkit.ParserStereoOrderErrorKind attribute) ProbeMemberMissing (cosmolkit.ParserStereoOrderErrorKind attribute) problem_atoms (cosmolkit.KekulizeError property) problems (cosmolkit.ChemistryProblemReport attribute) process_property_lists (cosmolkit.SdfReadParams attribute) Processing (cosmolkit.MolPostErrorKind attribute) product (cosmolkit.ReactionApplyError property) Product (cosmolkit.ReactionApplyErrorKind attribute) product (cosmolkit.ReactionParseError property) Product (cosmolkit.ReactionRole attribute) (cosmolkit.ReactionRunErrorKind attribute) product_atom (cosmolkit.ReactionProductError property) product_template() (cosmolkit.Reaction method) product_templates (cosmolkit.Reaction attribute) products (cosmolkit.ReactionApplyError property) profile (cosmolkit.OperationInvariantEntry attribute) (cosmolkit.ParityMatrixEntry attribute) progress (cosmolkit.McsError property) Progress (cosmolkit.McsErrorKind attribute) progress_bar (cosmolkit.BatchExportParams attribute) (cosmolkit.BatchParams attribute) (cosmolkit.BatchQueryParams attribute) (cosmolkit.MoleculeBatch attribute) progress_callback (cosmolkit.BatchQueryParams attribute) Projection (cosmolkit.ProteinReadErrorKind attribute) projection (cosmolkit.PruningError property) Projection (cosmolkit.PruningErrorKind attribute) Prop (cosmolkit.MmffParamTable attribute) prop() (cosmolkit.MoleculeProperties method) properties (cosmolkit.MmffOptimizationFailure property) Properties (cosmolkit.MmffOptimizationFailureKind attribute) properties (cosmolkit.Molecule attribute) (cosmolkit.MoleculeBuilder attribute) Properties (cosmolkit.SanitizeErrorKind attribute) PROPERTIES (cosmolkit.SanitizeOperations attribute) Properties (cosmolkit.SanitizeStage attribute) properties (cosmolkit.SdfRecord attribute) (cosmolkit.SmilesStereoError property) Properties (cosmolkit.SmilesStereoErrorKind attribute) properties (cosmolkit.TautomerMoleculeView attribute) Property (cosmolkit.AttachmentExpansionErrorKind attribute) property (cosmolkit.CanonicalRankError property) Property (cosmolkit.CipDescriptorErrorKind attribute) property (cosmolkit.CipLabelerError property) Property (cosmolkit.CxQueryLoweringErrorKind attribute) property (cosmolkit.DoubleBondStereoError property) Property (cosmolkit.DrawingErrorKind attribute) property (cosmolkit.MolPostError property) Property (cosmolkit.MolWriteErrorKind attribute) (cosmolkit.PdbWriteErrorKind attribute) property (cosmolkit.PotentialStereoError property) (cosmolkit.ReactionValidationError property) Property (cosmolkit.ReactionValidationErrorKind attribute) (cosmolkit.ScaffoldErrorKind attribute) property (cosmolkit.SdfWriteError property) Property (cosmolkit.SdfWriteErrorKind attribute) property (cosmolkit.SmartsWriteError property) Property (cosmolkit.SmartsWriteErrorKind attribute) property (cosmolkit.SubstructMatchError property) (cosmolkit.WedgeError property) Property (cosmolkit.XyzWriteErrorKind attribute) property() (cosmolkit.Molecule method) property_error (cosmolkit.CipDescriptorError property) (cosmolkit.Mol2ReadError property) (cosmolkit.MolWriteError property) (cosmolkit.PdbWriteError property) (cosmolkit.ScaffoldError property) property_string (cosmolkit.SubstructMatchError property) (cosmolkit.TautomerRunError property) property_value (cosmolkit.SdfWriteError property) property_value_to_text() (in module cosmolkit) PropertyCache (cosmolkit.Coordinate2DErrorKind attribute) PropertyCacheError PropertyCacheErrorKind (class in cosmolkit) PropertyInt (cosmolkit.MolProcessingErrorKind attribute) (cosmolkit.ReactionProductErrorKind attribute) PropertyInteger (cosmolkit.SubstructMatchErrorKind attribute) PropertyIntReadError PropertyIntReadErrorKind (class in cosmolkit) PropertyKind (cosmolkit.SmilesParseErrorKind attribute) PropertyListCount (cosmolkit.SdfReadErrorKind attribute) PropertyString (cosmolkit.AtomCodeErrorKind attribute) (cosmolkit.DrawingErrorKind attribute) (cosmolkit.Mol2ReadErrorKind attribute) (cosmolkit.MolProcessingErrorKind attribute) (cosmolkit.MorganErrorKind attribute) (cosmolkit.ParserCarrierErrorKind attribute) (cosmolkit.StereoReadErrorKind attribute) (cosmolkit.SubstructMatchErrorKind attribute) (cosmolkit.TautomerRunErrorKind attribute) PropertyStringError PropertyStringErrorKind (class in cosmolkit) PropertyUInt (cosmolkit.PdbPostprocessErrorKind attribute) (cosmolkit.ReactionProductErrorKind attribute) PropertyUIntReadError PropertyUIntReadErrorKind (class in cosmolkit) PropertyULongReadError PropertyULongReadErrorKind (class in cosmolkit) PropertyValue (class in cosmolkit) (cosmolkit.AtomQueryPredicateKind attribute) (cosmolkit.BondQueryPredicateKind attribute) (cosmolkit.MolProcessingErrorKind attribute) (cosmolkit.SdfWriteErrorKind attribute) (cosmolkit.SmartsWriteErrorKind attribute) PropertyValueError PropertyValueKind (class in cosmolkit) props (cosmolkit.MoleculeProperties attribute) Protein (class in cosmolkit) (cosmolkit.BioOperationErrorKind attribute) (cosmolkit.ChainKind attribute) protein() (cosmolkit.BioStructure method) protein_from_mmcif() (in module cosmolkit) protein_from_pdb() (in module cosmolkit) ProteinAtomRef (class in cosmolkit) ProteinChainRef (class in cosmolkit) ProteinDnaComplex (cosmolkit.ChainKind attribute) ProteinProjectionError ProteinProjectionErrorKind (class in cosmolkit) ProteinReadError ProteinReadErrorKind (class in cosmolkit) ProteinResidueRef (class in cosmolkit) ProteinRnaComplex (cosmolkit.ChainKind attribute) ProteinSelectionSummary (class in cosmolkit) Protocol (cosmolkit.FingerprintWorkerErrorKind attribute) ProtocolDebt (cosmolkit.CanonicalRankErrorKind attribute) proximity_bonding (cosmolkit.BioMoleculeParams attribute) prune_rms_thresh (cosmolkit.EmbedParams attribute) pruning (cosmolkit.GenerationError property) Pruning (cosmolkit.GenerationErrorKind attribute) PruningError PruningErrorKind (class in cosmolkit) PSU (cosmolkit.ResidueCode attribute) PT (cosmolkit.Element attribute) PTR (cosmolkit.ResidueCode attribute) PU (cosmolkit.Element attribute) PYL (cosmolkit.ResidueCode attribute) PYR (cosmolkit.ResidueInfoKind attribute) Q qed() (cosmolkit.Molecule method) QUADRUPLE (cosmolkit.BondOrder attribute) Quadruple (cosmolkit.BondOrder attribute) quantity (cosmolkit.TransformError property) Query (cosmolkit.AttachmentExpansionErrorKind attribute) query (cosmolkit.CompiledQuery attribute) Query (cosmolkit.LayeredFingerprintErrorKind attribute) query (cosmolkit.McsResult attribute) Query (cosmolkit.PatternFingerprintErrorKind attribute) (cosmolkit.TopologicalFingerprintErrorKind attribute) query_atom (cosmolkit.MolWriteError property) (cosmolkit.SubstructMatchError property) query_atom_conversion (cosmolkit.MolPostError property) query_atoms (cosmolkit.SubstructMatchError property) query_bond (cosmolkit.SubstructMatchError property) query_compile (cosmolkit.TautomerRunError property) query_compile_error (cosmolkit.TautomerTransformError property) query_context (cosmolkit.SubstructMatchError property) query_graph (cosmolkit.AlignmentError property) (cosmolkit.MolWriteError property) (cosmolkit.PathError property) (cosmolkit.RecursiveStructureQuery attribute) (cosmolkit.SdfRecord attribute) query_mapping (cosmolkit.SubstructMatchError property) query_parse (cosmolkit.AlignmentError property) query_smarts (cosmolkit.MolWriteError property) query_state (cosmolkit.AromaticityError property) (cosmolkit.CipRankError property) (cosmolkit.HydrogenError property) (cosmolkit.KekulizeError property) (cosmolkit.MolWriteError property) QueryArithmetic (cosmolkit.ReactionValidationErrorKind attribute) QueryAtom (class in cosmolkit) (cosmolkit.MolProcessingErrorKind attribute) (cosmolkit.MolWriteErrorKind attribute) QueryAtomConversion (cosmolkit.MolPostErrorKind attribute) QueryAtomConversionError QueryAtomConversionErrorKind (class in cosmolkit) QueryBuildFailed (cosmolkit.CrystalffTorsionPreferencesErrorKind attribute) QueryCarrier (cosmolkit.PatternFingerprintErrorKind attribute) QueryCompile (cosmolkit.MaccsFingerprintErrorKind attribute) (cosmolkit.PatternFingerprintErrorKind attribute) (cosmolkit.TautomerRunErrorKind attribute) (cosmolkit.TautomerTransformErrorKind attribute) QueryCompileError QueryCompileErrorKind (class in cosmolkit) QueryContext (cosmolkit.MaccsFingerprintErrorKind attribute) (cosmolkit.PatternFingerprintErrorKind attribute) (cosmolkit.SubstructMatchErrorKind attribute) QueryGraph (class in cosmolkit) (cosmolkit.AlignmentErrorKind attribute) (cosmolkit.MolProcessingErrorKind attribute) (cosmolkit.MolWriteErrorKind attribute) (cosmolkit.PathErrorKind attribute) (cosmolkit.SdfErrorKind attribute) (cosmolkit.SdfReadErrorKind attribute) (cosmolkit.SmartsParseErrorKind attribute) QueryGraphCxExtensionsUnsupported (cosmolkit.SmartsWriteErrorKind attribute) QueryGraphError QueryGraphErrorKind (class in cosmolkit) QueryGraphTraversalUnsupported (cosmolkit.SmartsWriteErrorKind attribute) QueryMatchContext (cosmolkit.MorganErrorKind attribute) QueryMatchContextError QueryMatchContextErrorKind (class in cosmolkit) QueryParse (cosmolkit.AlignmentErrorKind attribute) QueryReactantBond (cosmolkit.ReactionProductErrorKind attribute) QueryRecord (cosmolkit.SdfErrorKind attribute) (cosmolkit.SdfReadErrorKind attribute) QuerySmarts (cosmolkit.MolWriteErrorKind attribute) QueryState (cosmolkit.MolProcessingErrorKind attribute) (cosmolkit.MolWriteErrorKind attribute) QueryStateError QueryStateErrorKind (class in cosmolkit) questions (cosmolkit.KekulizeError property) QuestionSubsetOverflow (cosmolkit.KekulizeErrorKind attribute) QUINTUPLE (cosmolkit.BondOrder attribute) Quintuple (cosmolkit.BondOrder attribute) QuotaExceeded (cosmolkit.IoErrorKind attribute) R R (cosmolkit.CipDescriptor attribute) r (cosmolkit.CipDescriptor attribute) R0AF (cosmolkit.ResidueCode attribute) R0TD (cosmolkit.ResidueCode attribute) R12P (cosmolkit.ResidueCode attribute) R144 (cosmolkit.ResidueCode attribute) R15P (cosmolkit.ResidueCode attribute) R16D (cosmolkit.ResidueCode attribute) R1BO (cosmolkit.ResidueCode attribute) R1MA (cosmolkit.ResidueCode attribute) R1MG (cosmolkit.ResidueCode attribute) R1PS (cosmolkit.ResidueCode attribute) R2MA (cosmolkit.ResidueCode attribute) R2MG (cosmolkit.ResidueCode attribute) R2OS (cosmolkit.ResidueCode attribute) R310 (cosmolkit.BioHelixClass attribute) R3CO (cosmolkit.ResidueCode attribute) R3DR (cosmolkit.ResidueCode attribute) R3FG (cosmolkit.ResidueCode attribute) R3NI (cosmolkit.ResidueCode attribute) R4OC (cosmolkit.ResidueCode attribute) R4SU (cosmolkit.ResidueCode attribute) R5BU (cosmolkit.ResidueCode attribute) R5CM (cosmolkit.ResidueCode attribute) R5MU (cosmolkit.ResidueCode attribute) R6MZ (cosmolkit.ResidueCode attribute) R7MG (cosmolkit.ResidueCode attribute) R8OG (cosmolkit.ResidueCode attribute) r_all (cosmolkit.BioBasicRefinementInfo attribute) r_free (cosmolkit.BioBasicRefinementInfo attribute) r_merge (cosmolkit.BioReflectionsInfo attribute) r_sym (cosmolkit.BioReflectionsInfo attribute) r_work (cosmolkit.BioBasicRefinementInfo attribute) RA (cosmolkit.Element attribute) radical (cosmolkit.OperationError property) Radical (cosmolkit.OperationErrorKind attribute) radical_electrons (cosmolkit.Atom attribute) (cosmolkit.MoleculeAtom attribute) (cosmolkit.QueryAtom attribute) RadicalCountOutOfRange (cosmolkit.RadicalErrorKind attribute) RadicalError RadicalErrorKind (class in cosmolkit) RADICALS (cosmolkit.CxSmilesFields attribute) Radicals (cosmolkit.SanitizeErrorKind attribute) radicals (cosmolkit.ScaffoldError property) Radicals (cosmolkit.ScaffoldErrorKind attribute) radius (cosmolkit.MorganFingerprintParams attribute) (cosmolkit.MorganGeneratorParams attribute) (cosmolkit.MorganSettings attribute) RAISE (cosmolkit.BatchErrorMode attribute) RAlpha (cosmolkit.BioHelixClass attribute) rand_neg_eig (cosmolkit.EmbedParams attribute) random_seed (cosmolkit.EmbedParams attribute) random_source (cosmolkit.StereoisomerOptions attribute) RandomBitsSource (cosmolkit.EnumerationErrorKind attribute) RandomSmilesWriteParams (class in cosmolkit) RandomSourcePoisoned (cosmolkit.EnumerationErrorKind attribute) Range (cosmolkit.AtomQueryPredicateKind attribute) RangeError (cosmolkit.FingerprintErrorKind attribute) Rank (cosmolkit.FragmentWriteInputErrorKind attribute) (cosmolkit.PotentialStereoErrorKind attribute) RankCount (cosmolkit.DoubleBondStereoErrorKind attribute) (cosmolkit.MoleculeHashErrorKind attribute) raw (cosmolkit.StereoOrderError property) raw_os_error (cosmolkit.IoError property) raw_remarks (cosmolkit.BioStructureSourceState attribute) RB (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) rb0 (cosmolkit.ElementInfo attribute) Rdkit (cosmolkit.AromaticityModel attribute) rdkit_function (cosmolkit.SubstructMatchError property) rdkit_version (cosmolkit.ParityMatrixEntry attribute) RdkitLike (cosmolkit.ValenceModel attribute) RE (cosmolkit.Element attribute) reactant (cosmolkit.ReactionParseError property) Reactant (cosmolkit.ReactionRole attribute) reactant (cosmolkit.ReactionRunError property) reactant_atom (cosmolkit.ReactionProductError property) reactant_template() (cosmolkit.Reaction method) reactant_templates (cosmolkit.Reaction attribute) ReactantArity (cosmolkit.ReactionRunErrorKind attribute) reactants (cosmolkit.ReactionApplyError property) ReactantTemplateIndex (cosmolkit.ReactionRunErrorKind attribute) Reaction (class in cosmolkit) reaction (cosmolkit.ReactionTemplateRemoval attribute) reaction_apply (cosmolkit.OperationError property) reaction_from_smirks() (in module cosmolkit) reaction_products() (cosmolkit.Molecule method) reaction_products_from_inputs() (cosmolkit.Molecule method) reaction_products_with_params() (cosmolkit.Molecule method) reaction_run (cosmolkit.OperationError property) ReactionApply (cosmolkit.OperationErrorKind attribute) ReactionApplyError ReactionApplyErrorKind (class in cosmolkit) ReactionApplyParams (class in cosmolkit) ReactionApplyResult (class in cosmolkit) ReactionCoordinateSelection (class in cosmolkit) ReactionInitializationError ReactionInitializationErrorKind (class in cosmolkit) ReactionModelError ReactionModelErrorKind (class in cosmolkit) ReactionParseError ReactionParseErrorKind (class in cosmolkit) ReactionParseParams (class in cosmolkit) ReactionProductError ReactionProductErrorKind (class in cosmolkit) ReactionRole (class in cosmolkit) ReactionRun (cosmolkit.OperationErrorKind attribute) ReactionRunError ReactionRunErrorKind (class in cosmolkit) ReactionRunParams (class in cosmolkit) ReactionSingleRunParams (class in cosmolkit) ReactionTemplateRemoval (class in cosmolkit) ReactionTemplateRemovalParams (class in cosmolkit) ReactionValidationError ReactionValidationErrorKind (class in cosmolkit) ReactionValidationIssue (class in cosmolkit) ReactionValidationIssueKind (class in cosmolkit) ReactionValidationParams (class in cosmolkit) ReactionValidationReport (class in cosmolkit) ReactionValidationSeverity (class in cosmolkit) ReactionWriteError ReactionWriteErrorKind (class in cosmolkit) ReactionWriteParams (class in cosmolkit) Read (cosmolkit.SdfErrorKind attribute) read() (cosmolkit.BioStructure static method) (cosmolkit.Protein static method) read_mol() (cosmolkit.Molecule static method) read_mol2() (cosmolkit.Molecule static method) read_mol2_with_params() (cosmolkit.Molecule static method) read_mol_with_params() (cosmolkit.Molecule static method) read_sdf() (cosmolkit.Molecule static method) (cosmolkit.MoleculeBatch static method) read_sdf_with_params() (cosmolkit.Molecule static method) (cosmolkit.MoleculeBatch static method) read_with_format() (cosmolkit.BioStructure static method) (cosmolkit.Protein static method) read_xyz() (cosmolkit.Molecule static method) ReadOnlyFilesystem (cosmolkit.IoErrorKind attribute) reason (cosmolkit.AvalonEngineError property) (cosmolkit.CanonicalRankError property) (cosmolkit.CrystalffTorsionPreferencesError property) (cosmolkit.DrawingError property) (cosmolkit.FingerprintError property) (cosmolkit.HydrogenError property) (cosmolkit.LayeredFingerprintError property) (cosmolkit.MaccsFingerprintError property) (cosmolkit.PatternFingerprintError property) (cosmolkit.PotentialStereoError property) (cosmolkit.RingFindingError property) (cosmolkit.ThreadCountError property) (cosmolkit.TopologicalFingerprintError property) (cosmolkit.UnsupportedFeatureError attribute) (cosmolkit.ValenceError property) reassign_stereo (cosmolkit.TautomerParams attribute) recalculated_implicit_valence (cosmolkit.AdjustHsError property) reciprocal_cosines (cosmolkit.BioCrystalInfo attribute) reciprocal_lengths (cosmolkit.BioCrystalInfo attribute) Record (cosmolkit.BioPdbReadStage attribute) record (cosmolkit.CxQueryLoweringError property) Record (cosmolkit.SdfReadErrorKind attribute) record() (cosmolkit.SdfDataset method) record_count (cosmolkit.SdfReadError property) record_errors (cosmolkit.BatchValidationError property) record_len (cosmolkit.PdbCisPepRecordError attribute) record_length (cosmolkit.PdbRemark350Error attribute) record_tag (cosmolkit.BioPdbReadError property) record_text() (cosmolkit.SdfDataset method) record_with_params() (cosmolkit.SdfDataset method) RecordIndexOutOfRange (cosmolkit.SdfReadErrorKind attribute) records (cosmolkit.MoleculeBatch attribute) records_consumed (cosmolkit.SdfRecordStream attribute) recursion_possible (cosmolkit.SubstructMatchParams attribute) RecursiveSmarts (cosmolkit.AtomQueryPredicateKind attribute) RecursiveStructureQuery (class in cosmolkit) redundancy (cosmolkit.BioReflectionsInfo attribute) reference (cosmolkit.DoubleBondStereoError property) (cosmolkit.FunctionStatus attribute) (cosmolkit.StereoOrderError property) reference_atom (cosmolkit.AlignmentAtomMap attribute) reference_conformer_id (cosmolkit.AlignmentParameters attribute) (cosmolkit.BestAlignmentParameters attribute) (cosmolkit.ConformerRmsd attribute) (cosmolkit.CoordinateRmsdParameters attribute) reference_position (cosmolkit.StereoOrderError property) ReferenceAtomOutOfRange (cosmolkit.AlignmentErrorKind attribute) refine (cosmolkit.BioMmcifWriteParams attribute) refinement (cosmolkit.BioMetadata attribute) Refinement (cosmolkit.BioMmcifReadStage attribute) (cosmolkit.BioSoftwareClassification attribute) RefinementDidNotConverge (cosmolkit.PotentialStereoErrorKind attribute) reflect (cosmolkit.AlignmentParameters attribute) (cosmolkit.BestAlignmentParameters attribute) (cosmolkit.ConformerAlignmentParameters attribute) reflection_count (cosmolkit.BioBasicRefinementInfo attribute) reflections (cosmolkit.BioExperimentInfo attribute) Reflections (cosmolkit.BioMmcifReadStage attribute) reflects_microhetero (cosmolkit.BioEntityRow attribute) reflns (cosmolkit.BioMmcifWriteParams attribute) relative (cosmolkit.ForceFieldAngleConstraintParams attribute) (cosmolkit.ForceFieldDistanceConstraintParams attribute) (cosmolkit.ForceFieldTorsionConstraintParams attribute) RelevantCycleCountOutOfRange (cosmolkit.RingFindingErrorKind attribute) RelevantCycleCountOverflow (cosmolkit.RingDecomposerErrorKind attribute) remaining (cosmolkit.SearchMcsError property) remark (cosmolkit.PdbReaderCause property) Remark (cosmolkit.PdbReaderCauseKind attribute) remark200 (cosmolkit.PdbRemarkFinalizationError attribute) Remark200 (cosmolkit.PdbRemarkFinalizationErrorKind attribute) remark3 (cosmolkit.PdbRemarkFinalizationError attribute) Remark3 (cosmolkit.PdbRemarkFinalizationErrorKind attribute) remark350 (cosmolkit.PdbRemarkFinalizationError attribute) Remark350 (cosmolkit.PdbRemarkFinalizationErrorKind attribute) remark_300_detail (cosmolkit.BioMetadata attribute) remark_length (cosmolkit.PdbRemarkMetadataError attribute) remark_metadata (cosmolkit.PdbRemarkFinalizationError attribute) RemarkMetadata (cosmolkit.PdbRemarkFinalizationErrorKind attribute) remarks (cosmolkit.BioRefinementInfo attribute) (cosmolkit.PdbStructureFinalizationError attribute) Remarks (cosmolkit.PdbStructureFinalizationErrorKind attribute) remove_and_track_isotopes (cosmolkit.RemoveHsParams attribute) remove_bond_between_atoms() (cosmolkit.MoleculeBuilder method) remove_bond_stereo (cosmolkit.TautomerParams attribute) remove_defining_bond_stereo (cosmolkit.RemoveHsParams attribute) remove_degree_zero (cosmolkit.RemoveHsParams attribute) remove_dummy_neighbors (cosmolkit.RemoveHsParams attribute) remove_higher_degrees (cosmolkit.RemoveHsParams attribute) remove_hs (cosmolkit.BioMoleculeParams attribute) (cosmolkit.InchiReadParams attribute) (cosmolkit.Mol2ReadParams attribute) (cosmolkit.SdfReadParams attribute) (cosmolkit.SmilesParseParams attribute) remove_hydrides (cosmolkit.RemoveHsParams attribute) remove_hydrogens_() (cosmolkit.Molecule method) remove_hydrogens_with_params_() (cosmolkit.Molecule method) remove_in_sgroups (cosmolkit.RemoveHsParams attribute) remove_isotopes (cosmolkit.RemoveHsParams attribute) remove_isotopic_hydrogens (cosmolkit.TautomerParams attribute) remove_mapped (cosmolkit.RemoveHsParams attribute) remove_nonimplicit (cosmolkit.RemoveHsParams attribute) remove_nontetrahedral_neighbors (cosmolkit.RemoveHsParams attribute) remove_only_h_neighbors (cosmolkit.RemoveHsParams attribute) remove_sp3_stereo (cosmolkit.TautomerParams attribute) remove_unmatched_atoms (cosmolkit.ReactionApplyParams attribute) remove_with_query (cosmolkit.RemoveHsParams attribute) remove_with_wedged_bond (cosmolkit.RemoveHsParams attribute) removed_templates (cosmolkit.ReactionTemplateRemoval attribute) RemovedCenter (cosmolkit.StereoOrderErrorKind attribute) RemovedLigand (cosmolkit.StereoOrderErrorKind attribute) RemoveHsParams (class in cosmolkit) Replace3DCoordinatesParams (class in cosmolkit) replace_existing_tags (cosmolkit.StructureTagParams attribute) ReplacementCycle (cosmolkit.SmilesParseErrorKind attribute) replacements (cosmolkit.ReactionParseParams attribute) (cosmolkit.SmartsParseParams attribute) (cosmolkit.SmilesParseParams attribute) report (cosmolkit.ReactionInitializationError property) report_path (cosmolkit.BatchImageParams attribute) reported_angle (cosmolkit.BioCisPep attribute) reported_distance (cosmolkit.BioConnection attribute) reported_sym (cosmolkit.BioConnection attribute) representation (cosmolkit.MolPostError property) Representation (cosmolkit.MolPostErrorKind attribute) RepresentativeHelical (cosmolkit.BioAssemblySpecialKind attribute) requested (cosmolkit.ForceFieldError property) (cosmolkit.MmffForceFieldError property) (cosmolkit.StereoError property) (cosmolkit.UffEvaluationFailure attribute) (cosmolkit.UffForceFieldError property) (cosmolkit.UffOptimizationErrorKind attribute) requested_num_confs (cosmolkit.EmbedMultipleConfsResult attribute) RequestedMappingMissing (cosmolkit.NonbondedFragmentMappingErrorKind attribute) Require2D (cosmolkit.SdfCoordinateMode attribute) Require3D (cosmolkit.SdfCoordinateMode attribute) required (cosmolkit.TopologicalTorsionPathScoreError property) (cosmolkit.TransformError property) required_len (cosmolkit.PdbCisPepRecordError attribute) RequiredFieldsPastRecord (cosmolkit.PdbCisPepRecordErrorKind attribute) RequiredNow (cosmolkit.ParityPolicy attribute) RequiredPropertyStringError RequiredPropertyStringErrorKind (class in cosmolkit) RequiredWhenSupported (cosmolkit.ParityPolicy attribute) requirement (cosmolkit.OperationError property) RequireZero (cosmolkit.CoordinateZPolicy attribute) res_begin (cosmolkit.BioTlsSelection attribute) res_end (cosmolkit.BioTlsSelection attribute) res_id (cosmolkit.BioModRes attribute) ReservedAtomPropertyKey (cosmolkit.OperationErrorKind attribute) residue (cosmolkit.AtomAddress attribute) (cosmolkit.BioSiftsUnpResidue attribute) Residue (cosmolkit.MmcifCcdRestoreErrorKind attribute) residue (cosmolkit.ProteinAtomRef attribute) residue() (cosmolkit.BioStructure method) residue_address (cosmolkit.PdbHelixError attribute) (cosmolkit.PdbModResError attribute) residue_atoms() (cosmolkit.BioStructure method) residue_code() (in module cosmolkit) residue_id (cosmolkit.BioAtom attribute) (cosmolkit.BioAtomRow attribute) residue_info() (in module cosmolkit) residue_info_checked() (in module cosmolkit) residue_info_kind (cosmolkit.BioResidue attribute) (cosmolkit.BioResidueRow attribute) residue_key (cosmolkit.PdbAtomFieldError attribute) residue_span (cosmolkit.BioChain attribute) (cosmolkit.BioChainRow attribute) ResidueAddress (class in cosmolkit) (cosmolkit.PdbCisPepRecordErrorKind attribute) (cosmolkit.PdbHelixErrorKind attribute) (cosmolkit.PdbLinkRecordErrorKind attribute) (cosmolkit.PdbModResErrorKind attribute) (cosmolkit.PdbSheetErrorKind attribute) (cosmolkit.PdbSsbondRecordErrorKind attribute) ResidueAddressNotRepresentable (cosmolkit.MmcifAtomSiteGroupingErrorKind attribute) (cosmolkit.MmcifCisPepErrorKind attribute) (cosmolkit.MmcifConnectionErrorKind attribute) (cosmolkit.MmcifHelixErrorKind attribute) (cosmolkit.MmcifModResErrorKind attribute) (cosmolkit.MmcifSheetErrorKind attribute) ResidueCode (class in cosmolkit) ResidueCodeParseError ResidueIdentity (class in cosmolkit) ResidueInfo (class in cosmolkit) ResidueInfoKind (class in cosmolkit) ResidueKey (cosmolkit.PdbAtomFieldErrorKind attribute) ResidueKind (class in cosmolkit) ResidueName (cosmolkit.ChemCompModelErrorKind attribute) ResidueNameNotAscii (cosmolkit.PdbResidueKeyErrorKind attribute) ResidueNameNotRepresentable (cosmolkit.MmcifAtomSiteGroupingErrorKind attribute) (cosmolkit.MmcifCisPepErrorKind attribute) (cosmolkit.MmcifConnectionErrorKind attribute) (cosmolkit.MmcifHelixErrorKind attribute) (cosmolkit.MmcifModResErrorKind attribute) (cosmolkit.MmcifSheetErrorKind attribute) ResidueNameTooWide (cosmolkit.PdbResidueKeyErrorKind attribute) residues (cosmolkit.BioChain attribute) (cosmolkit.BioStructure attribute) (cosmolkit.BioStructureParts attribute) (cosmolkit.Protein attribute) (cosmolkit.ProteinChainRef attribute) (cosmolkit.ProteinSelectionSummary attribute) ResidueSequenceError ResidueSequenceErrorKind (class in cosmolkit) ResidueSourceIds (class in cosmolkit) ResidueSourceIdsNotRepresentable (cosmolkit.MmcifAtomSiteGroupingErrorKind attribute) resolution (cosmolkit.BioStructure attribute) (cosmolkit.BioStructureSourceState attribute) resolution_high (cosmolkit.BioBasicRefinementInfo attribute) (cosmolkit.BioReflectionsInfo attribute) resolution_low (cosmolkit.BioBasicRefinementInfo attribute) (cosmolkit.BioReflectionsInfo attribute) ResourceBusy (cosmolkit.IoErrorKind attribute) restr_stats (cosmolkit.BioRefinementInfo attribute) result_slots (cosmolkit.SerialResultCapacityError property) result_type (cosmolkit.MoleculeOpSpec attribute) ResultCapacity (cosmolkit.SerialConformerOptimizationErrorKind attribute) ResultContextMissing (cosmolkit.McsErrorKind attribute) ResultInvariant (cosmolkit.EmbedSeedErrorKind attribute) ResultQueryGraph (cosmolkit.McsErrorKind attribute) ResultSmarts (cosmolkit.McsErrorKind attribute) ResultValueOutOfRange (cosmolkit.McsErrorKind attribute) retain_selection_() (cosmolkit.BioStructure method) (cosmolkit.Protein method) return_code (cosmolkit.InchiResult attribute) RF (cosmolkit.Element attribute) rfree_selection_method (cosmolkit.BioRefinementInfo attribute) rfree_set_count (cosmolkit.BioBasicRefinementInfo attribute) RG (cosmolkit.Element attribute) RGamma (cosmolkit.BioHelixClass attribute) RGroupLabel (cosmolkit.AtomQueryPredicateKind attribute) RH (cosmolkit.Element attribute) right (cosmolkit.FingerprintError property) (cosmolkit.PatternFingerprintError property) Ring (cosmolkit.DescriptorErrorKind attribute) (cosmolkit.FragmentWriteInputErrorKind attribute) ring (cosmolkit.McsError property) Ring (cosmolkit.PotentialStereoErrorKind attribute) ring (cosmolkit.SmartsParseError property) (cosmolkit.TautomerScore attribute) ring_atom_count (cosmolkit.AromaticityError property) ring_bond_count (cosmolkit.AromaticityError property) ring_decomposer (cosmolkit.RingFindingError property) ring_finding (cosmolkit.AromaticityError property) (cosmolkit.CipLabelerError property) (cosmolkit.KekulizeError property) (cosmolkit.LegacyStereoError property) (cosmolkit.MmffMolPropertiesError property) (cosmolkit.ReactionProductError property) (cosmolkit.WedgeError property) ring_index (cosmolkit.AromaticityError property) ring_matches_ring_only (cosmolkit.McsAtomCompareParameters attribute) (cosmolkit.McsBondCompareParameters attribute) RING_PATH (cosmolkit.AvalonFingerprintFlags attribute) RING_PATTERN (cosmolkit.AvalonFingerprintFlags attribute) RING_PRESENCE (cosmolkit.LayeredFingerprintLayers attribute) ring_relations (cosmolkit.PotentialStereoResult attribute) RING_SIZE (cosmolkit.LayeredFingerprintLayers attribute) RING_SIZE_COUNTS (cosmolkit.AvalonFingerprintFlags attribute) RingAtomOutOfRange (cosmolkit.AromaticityErrorKind attribute) (cosmolkit.AtropisomerErrorKind attribute) (cosmolkit.RingFindingErrorKind attribute) RingAtomRowCount (cosmolkit.AtropisomerErrorKind attribute) RingBondCount (cosmolkit.AtomQueryPredicateKind attribute) (cosmolkit.AtomRangeDataFunctionKind attribute) RingBondCountLessEqual (cosmolkit.AtomQueryPredicateKind attribute) RingBondNotMovable (cosmolkit.TransformErrorKind attribute) RingBondOutOfRange (cosmolkit.AromaticityErrorKind attribute) (cosmolkit.AtropisomerErrorKind attribute) (cosmolkit.RingFindingErrorKind attribute) RingBondRowCount (cosmolkit.AtropisomerErrorKind attribute) RingDecomposer (cosmolkit.RingFindingErrorKind attribute) RingDecomposerError RingDecomposerErrorKind (class in cosmolkit) RingFamilyEdgeMappingMissing (cosmolkit.RingFindingErrorKind attribute) RingFinding (cosmolkit.AromaticityErrorKind attribute) (cosmolkit.AtropisomerErrorKind attribute) (cosmolkit.CanonicalRankErrorKind attribute) (cosmolkit.CipLabelerErrorKind attribute) (cosmolkit.Coordinate2DErrorKind attribute) (cosmolkit.KekulizeErrorKind attribute) (cosmolkit.LegacyStereoErrorKind attribute) (cosmolkit.MmffMolPropertiesErrorKind attribute) (cosmolkit.ReactionProductErrorKind attribute) (cosmolkit.WedgeErrorKind attribute) RingFindingError RingFindingErrorKind (class in cosmolkit) RingInfoDimensionMismatch (cosmolkit.AromaticityErrorKind attribute) RingInfoNotInitialized (cosmolkit.AromaticityErrorKind attribute) (cosmolkit.DoubleBondStereoErrorKind attribute) RingInfoNotSssr (cosmolkit.AtropisomerErrorKind attribute) RingInfoUnavailable (cosmolkit.CrystalffTorsionPreferencesErrorKind attribute) RingInitialization (cosmolkit.Coordinate2DTemplateErrorKind attribute) RingMembershipMissing (cosmolkit.McsErrorKind attribute) RingMembershipRows (cosmolkit.QueryMatchContextErrorKind attribute) RingOutOfRange (cosmolkit.McsErrorKind attribute) RingPrecondition (cosmolkit.QueryMatchContextErrorKind attribute) RingPreparation (cosmolkit.FingerprintPreparationErrorKind attribute) RingRowCount (cosmolkit.DoubleBondStereoErrorKind attribute) RingRowLengthMismatch (cosmolkit.AromaticityErrorKind attribute) RingRows (cosmolkit.SmilesStereoErrorKind attribute) rings (cosmolkit.BoundsQueryError property) Rings (cosmolkit.BoundsQueryErrorKind attribute) rings (cosmolkit.CanonicalRankError property) Rings (cosmolkit.DoubleBondStereoErrorKind attribute) rings (cosmolkit.EnumerationError property) Rings (cosmolkit.EnumerationErrorKind attribute) rings (cosmolkit.GenerationError property) Rings (cosmolkit.GenerationErrorKind attribute) (cosmolkit.LayeredFingerprintErrorKind attribute) (cosmolkit.MaccsFingerprintErrorKind attribute) rings (cosmolkit.MmffBuilderError property) Rings (cosmolkit.MmffBuilderErrorKind attribute) (cosmolkit.MolecularForceFieldErrorKind attribute) (cosmolkit.MolProcessingErrorKind attribute) rings (cosmolkit.OperationError property) Rings (cosmolkit.OperationErrorKind attribute) (cosmolkit.PatternFingerprintErrorKind attribute) (cosmolkit.QueryMatchContextErrorKind attribute) (cosmolkit.SanitizeErrorKind attribute) rings (cosmolkit.ScaffoldError property) Rings (cosmolkit.ScaffoldErrorKind attribute) rings (cosmolkit.SmilesStereoError property) Rings (cosmolkit.SmilesStereoErrorKind attribute) (cosmolkit.StereoReadErrorKind attribute) rings (cosmolkit.TautomerRunError property) Rings (cosmolkit.TautomerRunErrorKind attribute) (cosmolkit.UffOptimizationErrorKind attribute) RingSearchParams (class in cosmolkit) RingSearchResult (class in cosmolkit) RingStereoRelation (class in cosmolkit) RingTableLengthMismatch (cosmolkit.AromaticityErrorKind attribute) rmsd (cosmolkit.AlignmentResult attribute) (cosmolkit.ConformerRmsd attribute) rmsds (cosmolkit.ConformerAlignmentReport attribute) RN (cosmolkit.Element attribute) Rna (cosmolkit.ChainKind attribute) (cosmolkit.PolymerKind attribute) RNA (cosmolkit.ResidueInfoKind attribute) Rna (cosmolkit.ResidueKind attribute) role (cosmolkit.PathError property) (cosmolkit.ReactionModelError property) (cosmolkit.ReactionParseError property) (cosmolkit.ReactionValidationError property) (cosmolkit.ReactionValidationIssue attribute) (cosmolkit.ReactionWriteError property) (cosmolkit.TransformError property) (cosmolkit.UffBuilderError property) ROmega (cosmolkit.BioHelixClass attribute) root (cosmolkit.RingDecomposerError property) RootAtomNotSelected (cosmolkit.FragmentWriteInputErrorKind attribute) RootAtomOutOfRange (cosmolkit.FragmentWriteInputErrorKind attribute) RootAtomRequiresSingleFragment (cosmolkit.FragmentWriteInputErrorKind attribute) rooted_at_atom (cosmolkit.ReactionWriteParams attribute) (cosmolkit.SmartsWriteParams attribute) (cosmolkit.SmilesWriteParams attribute) RootedAtomOutOfRange (cosmolkit.SmartsWriteErrorKind attribute) RootNotObject (cosmolkit.MmjsonStructureErrorKind attribute) RotatableBondsOptions (class in cosmolkit) row (cosmolkit.AromaticityError property) (cosmolkit.BoundsMatrixError property) (cosmolkit.ChemCompAtomError property) (cosmolkit.Coordinate2DTemplateError property) (cosmolkit.CoordinateInputError property) (cosmolkit.DescriptorError property) (cosmolkit.DrawingError property) (cosmolkit.FragmentCoordinateViewError property) (cosmolkit.FullCopyComponentError property) (cosmolkit.MappingValidationError property) Row (cosmolkit.MatrixAxis attribute) row (cosmolkit.McsError property) (cosmolkit.OperationError property) (cosmolkit.PotentialStereoError property) (cosmolkit.ProteinAtomRef attribute) (cosmolkit.ProteinChainRef attribute) (cosmolkit.ProteinResidueRef attribute) (cosmolkit.SmartsWriteError property) (cosmolkit.TransformError property) (cosmolkit.XmlTextPos attribute) row_count (cosmolkit.OperationError property) row_index (cosmolkit.MmcifAtomSiteGroupingError property) (cosmolkit.MmcifAtomSiteRowOutOfBounds property) RowCount (cosmolkit.CoordinateInputErrorKind attribute) (cosmolkit.CoordinateValidationErrorKind attribute) RowCountOverflow (cosmolkit.MmjsonStructureErrorKind attribute) RowIndexTooLarge (cosmolkit.BioStructureErrorKind attribute) RowOverflow (cosmolkit.ReactionProductErrorKind attribute) RowReferenceOutOfBounds (cosmolkit.BioStructureErrorKind attribute) rows (cosmolkit.CoordinateValidationError property) (cosmolkit.StereoError property) RowSpanOutOfBounds (cosmolkit.BioStructureErrorKind attribute) RowSpanOverflow (cosmolkit.BioStructureErrorKind attribute) RPi (cosmolkit.BioHelixClass attribute) RU (cosmolkit.Element attribute) Rule4bInstanceNotInRuleSet (cosmolkit.CipLabelerErrorKind attribute) Rule5NewInstanceNotInRuleSet (cosmolkit.CipLabelerErrorKind attribute) run() (cosmolkit.Reaction method) S s (cosmolkit.BioTlsGroup attribute) S (cosmolkit.CipDescriptor attribute) s (cosmolkit.CipDescriptor attribute) S (cosmolkit.Element attribute) (cosmolkit.Hybridization attribute) SAC (cosmolkit.ResidueCode attribute) Saccharide (cosmolkit.ResidueKind attribute) SaccharideD (cosmolkit.PolymerKind attribute) SaccharideL (cosmolkit.PolymerKind attribute) SAL (cosmolkit.ResidueCode attribute) Same (cosmolkit.BioAsu attribute) same_orientation (cosmolkit.RingStereoRelation attribute) sample_seed (cosmolkit.Coordinate2DParams attribute) samples (cosmolkit.Coordinate2DParams attribute) sanitize (cosmolkit.AtomPathSubsetCopyError property) Sanitize (cosmolkit.AtomPathSubsetCopyErrorKind attribute) (cosmolkit.BioMoleculeConversionErrorKind attribute) sanitize (cosmolkit.BioMoleculeParams attribute) (cosmolkit.HydrogenError property) Sanitize (cosmolkit.HydrogenErrorKind attribute) sanitize (cosmolkit.InchiReadParams attribute) (cosmolkit.Mol2ReadParams attribute) Sanitize (cosmolkit.MolProcessingErrorKind attribute) sanitize (cosmolkit.OperationError property) Sanitize (cosmolkit.OperationErrorKind attribute) sanitize (cosmolkit.ReactionParseParams attribute) (cosmolkit.RemoveHsParams attribute) (cosmolkit.SdfReadParams attribute) Sanitize (cosmolkit.SmilesErrorKind attribute) sanitize (cosmolkit.SmilesParseParams attribute) (cosmolkit.TautomerRunError property) Sanitize (cosmolkit.TautomerRunErrorKind attribute) sanitize() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) sanitize_() (cosmolkit.Molecule method) sanitize_with_params() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) sanitize_with_params_() (cosmolkit.Molecule method) SanitizeError SanitizeErrorKind (class in cosmolkit) SanitizeFailed (cosmolkit.InchiErrorKind attribute) SanitizeOperations (class in cosmolkit) SanitizeParams (class in cosmolkit) SanitizeStage (class in cosmolkit) SAR (cosmolkit.ResidueCode attribute) SB (cosmolkit.Element attribute) SBT (cosmolkit.ResidueCode attribute) SC (cosmolkit.Element attribute) scaffold (cosmolkit.OperationError property) Scaffold (cosmolkit.OperationErrorKind attribute) SCAFFOLD_COLORS (cosmolkit.AvalonFingerprintFlags attribute) SCAFFOLD_IDS (cosmolkit.AvalonFingerprintFlags attribute) SCAFFOLD_LINKS (cosmolkit.AvalonFingerprintFlags attribute) ScaffoldError ScaffoldErrorKind (class in cosmolkit) scale (cosmolkit.BioMmcifWriteParams attribute) scattering_type (cosmolkit.BioDiffractionInfo attribute) SCH (cosmolkit.ResidueCode attribute) SCN (cosmolkit.ResidueCode attribute) score (cosmolkit.TautomerScoreTerm attribute) score_params (cosmolkit.TautomerParams attribute) ScoreCacheTargetMismatch (cosmolkit.TautomerRunErrorKind attribute) scorer (cosmolkit.TautomerParams attribute) SCY (cosmolkit.ResidueCode attribute) Sdf (cosmolkit.MolecularIoErrorKind attribute) sdf_data_fields (cosmolkit.MoleculeProperties attribute) sdf_property_lists (cosmolkit.MoleculeProperties attribute) SdfBatchIterator (class in cosmolkit) SdfCoordinateMode (class in cosmolkit) SdfDataset (class in cosmolkit) SdfDatasetIterator (class in cosmolkit) SdfError SdfErrorKind (class in cosmolkit) SdfFormat (class in cosmolkit) SdfGraph (class in cosmolkit) SdfGraph.Molecule (class in cosmolkit) SdfGraph.Query (class in cosmolkit) SdfPropertyList (class in cosmolkit) SdfPropertyListTarget (class in cosmolkit) SdfReader (class in cosmolkit) SdfReaderBatchIterator (class in cosmolkit) SdfReadError SdfReadErrorKind (class in cosmolkit) SdfReadParams (class in cosmolkit) SdfRecord (class in cosmolkit) SdfRecordMetadata (class in cosmolkit) SdfRecordStream (class in cosmolkit) SdfWriteError SdfWriteErrorKind (class in cosmolkit) SDS (cosmolkit.ResidueCode attribute) SE (cosmolkit.Element attribute) Search (cosmolkit.DescriptorErrorKind attribute) SearchMcsError SearchMcsErrorKind (class in cosmolkit) SEC (cosmolkit.ResidueCode attribute) second (cosmolkit.Coordinate2DLayoutError property) Second (cosmolkit.ForceFieldAngleIndexArgument attribute) (cosmolkit.ForceFieldBondIndexArgument attribute) (cosmolkit.ForceFieldTorsionIndexArgument attribute) second (cosmolkit.StereoOrderError property) (cosmolkit.TransformError property) Second (cosmolkit.UffInversionIndexArgument attribute) second_bond (cosmolkit.AdjacencyError property) (cosmolkit.TransformError property) second_component (cosmolkit.NonbondedFragmentMappingError property) second_position (cosmolkit.AdjacencyError property) (cosmolkit.MatrixError property) second_role (cosmolkit.TransformError property) section (cosmolkit.PickleError property) seed (cosmolkit.EmbedSeedError property) (cosmolkit.GenerationError property) Seed (cosmolkit.GenerationErrorKind attribute) SeedAtomMappingMissing (cosmolkit.SearchMcsErrorKind attribute) SeedAtomNotBondEndpoint (cosmolkit.SearchMcsErrorKind attribute) SeedBondAlreadyExcluded (cosmolkit.SearchMcsErrorKind attribute) SeedExcludedBondOutOfRange (cosmolkit.SearchMcsErrorKind attribute) SeedNewAtomMissing (cosmolkit.SearchMcsErrorKind attribute) SeedReconstructionBondMissing (cosmolkit.McsErrorKind attribute) SeedRemainingAtomUnderflow (cosmolkit.SearchMcsErrorKind attribute) SeedRemainingBondUnderflow (cosmolkit.SearchMcsErrorKind attribute) segment (cosmolkit.ResidueAddress attribute) (cosmolkit.ThreadCountError property) segment_id (cosmolkit.ResidueSourceIds attribute) SegmentNotAscii (cosmolkit.PdbResidueKeyErrorKind attribute) SegmentNotRepresentable (cosmolkit.PdbResidueKeyErrorKind attribute) SegmentTooWide (cosmolkit.PdbResidueKeyErrorKind attribute) select() (cosmolkit.MoleculeBatch method) selected_atom_ids() (cosmolkit.BioStructure method) (cosmolkit.Protein method) SelectedBondCopyError SelectedBondCopyErrorKind (class in cosmolkit) SelectedConformerCoordinateCountMismatch (cosmolkit.UffBuilderErrorKind attribute) SelectedConformerDuplicated (cosmolkit.FragmentCoordinateViewErrorKind attribute) SelectedConformerMissing (cosmolkit.FragmentCoordinateViewErrorKind attribute) (cosmolkit.SmilesStereoErrorKind attribute) SelectedSubstanceGroupCopyError SelectedSubstanceGroupCopyErrorKind (class in cosmolkit) SelectedThreeDimensionalConformerNotFound (cosmolkit.UffBuilderErrorKind attribute) Selection (cosmolkit.BioOperationErrorKind attribute) selection (cosmolkit.SmilesParseError property) selection_summary() (cosmolkit.Protein method) SelectionChainNotRepresentable (cosmolkit.MmcifTlsInfoErrorKind attribute) selections (cosmolkit.BioTlsGroup attribute) SelfLoop (cosmolkit.RingDecomposerErrorKind attribute) SelfLoopBond (cosmolkit.TopologyValidationErrorKind attribute) SelfRingClosure (cosmolkit.SmartsParseErrorKind attribute) SemanticPreconditionContract (cosmolkit.OperationErrorKind attribute) sense (cosmolkit.BioStrand attribute) SEP (cosmolkit.ResidueCode attribute) Separators (cosmolkit.ReactionParseErrorKind attribute) seq_begin (cosmolkit.BioEntityDbRef attribute) seq_end (cosmolkit.BioEntityDbRef attribute) seq_id (cosmolkit.MmcifSiftsUnpError property) (cosmolkit.ResidueSourceIds attribute) seq_num (cosmolkit.PdbSeqId attribute) SeqId (cosmolkit.AtomSiteIdentityField attribute) SeqidRange (cosmolkit.BioSelectionParseErrorKind attribute) sequence_id (cosmolkit.MmcifSequenceIdError property) sequence_number (cosmolkit.ResidueAddress attribute) sequence_offset (cosmolkit.PdbSheetError attribute) SequenceId (cosmolkit.MmcifAtomSiteGroupingErrorKind attribute) (cosmolkit.MmcifCisPepErrorKind attribute) (cosmolkit.MmcifConnectionErrorKind attribute) (cosmolkit.MmcifEntityInfoErrorKind attribute) (cosmolkit.MmcifHelixErrorKind attribute) (cosmolkit.MmcifModResErrorKind attribute) (cosmolkit.MmcifSheetErrorKind attribute) (cosmolkit.MmcifTlsInfoErrorKind attribute) SequenceIdNotRepresentable (cosmolkit.PdbResidueKeyErrorKind attribute) SequenceNotFound (cosmolkit.MmcifSiftsUnpErrorKind attribute) SequenceUtf8 (cosmolkit.MmcifCcdRestoreErrorKind attribute) SER (cosmolkit.ResidueCode attribute) SerdeJsonCategory (class in cosmolkit) SerdeJsonError serial (cosmolkit.AtomSourceIds attribute) (cosmolkit.BioPdbWriteError property) (cosmolkit.MmffOptimizationFailure property) Serial (cosmolkit.MmffOptimizationFailureKind attribute) (cosmolkit.UffPreparedOptimizationErrorKind attribute) serial_number (cosmolkit.RecursiveStructureQuery attribute) SerialConformerOptimizationError SerialConformerOptimizationErrorKind (class in cosmolkit) SerialCoordinateCountError SerialIncrementOverflow (cosmolkit.BioPdbWriteErrorKind attribute) SerialOffsetOverflow (cosmolkit.BioPdbWriteErrorKind attribute) SerialOutsideSourceDefinedRange (cosmolkit.MmcifAtomSiteScalarErrorKind attribute) (cosmolkit.PdbAtomFieldErrorKind attribute) SerialResultCapacityError SerialUffOptimizationError SerialUffOptimizationErrorKind (class in cosmolkit) set (cosmolkit.ReactionRunError property) set_2d_coordinates() (cosmolkit.MoleculeBuilder method) set_2d_coordinates_() (cosmolkit.Molecule method) set_2d_coordinates_with_params_() (cosmolkit.Molecule method) set_3d_coordinates_() (cosmolkit.Molecule method) set_3d_coordinates_with_params_() (cosmolkit.Molecule method) SET_AROMATICITY (cosmolkit.SanitizeOperations attribute) set_atom_formal_charge() (cosmolkit.MoleculeBuilder method) set_atom_position_() (cosmolkit.Molecule method) set_atom_position_with_params_() (cosmolkit.Molecule method) set_atom_property_bool_() (cosmolkit.Molecule method) set_atom_property_double_() (cosmolkit.Molecule method) set_atom_property_int_() (cosmolkit.Molecule method) set_atom_property_int_vector_() (cosmolkit.Molecule method) set_atom_property_string_() (cosmolkit.Molecule method) set_atom_property_string_vector_() (cosmolkit.Molecule method) set_atom_property_uint_() (cosmolkit.Molecule method) set_bits_per_feature() (cosmolkit.MorganSettings method) (cosmolkit.TopologicalTorsionSettings method) set_bond_order() (cosmolkit.MoleculeBuilder method) set_callback() (cosmolkit.TautomerParams method) SET_CONJUGATION (cosmolkit.SanitizeOperations attribute) set_count_bounds() (cosmolkit.MorganSettings method) (cosmolkit.TopologicalTorsionSettings method) set_count_simulation() (cosmolkit.MorganSettings method) (cosmolkit.TopologicalTorsionSettings method) set_fixed_atoms_() (cosmolkit.MolecularForceField method) set_fp_size() (cosmolkit.MorganSettings method) (cosmolkit.TopologicalTorsionSettings method) set_helix_class_as_int() (cosmolkit.BioHelix method) SET_HYBRIDIZATION (cosmolkit.SanitizeOperations attribute) set_include_chirality() (cosmolkit.MorganSettings method) (cosmolkit.TopologicalTorsionSettings method) set_include_redundant_environments() (cosmolkit.MorganSettings method) set_match_params() (cosmolkit.Reaction method) set_max_tautomers() (cosmolkit.TautomerParams method) set_max_transforms() (cosmolkit.TautomerParams method) set_only_3d_conformer_() (cosmolkit.Molecule method) set_only_3d_conformer_with_params_() (cosmolkit.Molecule method) set_only_bits (cosmolkit.LayeredFingerprintParams attribute) set_only_nonzero_invariants() (cosmolkit.MorganSettings method) set_only_shortest_paths() (cosmolkit.TopologicalTorsionSettings method) set_position_() (cosmolkit.MolecularForceField method) set_positions_() (cosmolkit.MolecularForceField method) set_radius() (cosmolkit.MorganSettings method) set_reassign_stereo() (cosmolkit.TautomerParams method) set_remove_bond_stereo() (cosmolkit.TautomerParams method) set_remove_isotopic_hydrogens() (cosmolkit.TautomerParams method) set_remove_sp3_stereo() (cosmolkit.TautomerParams method) set_scorer() (cosmolkit.TautomerParams method) set_torsion_atom_count() (cosmolkit.TopologicalTorsionSettings method) set_value() (cosmolkit.SparseCountFingerprint method) (cosmolkit.SparseCountFingerprint32 method) SetAromaticity (cosmolkit.SanitizeStage attribute) SetConjugation (cosmolkit.SanitizeStage attribute) SetHybridization (cosmolkit.SanitizeStage attribute) settings (cosmolkit.MorganFingerprintGenerator attribute) (cosmolkit.TopologicalTorsionFingerprintGenerator attribute) severity (cosmolkit.ReactionValidationIssue attribute) SF4 (cosmolkit.ResidueCode attribute) SG (cosmolkit.Element attribute) sgroup (cosmolkit.QueryGraphError property) (cosmolkit.TopologyValidationError property) SGroupBondMembership (cosmolkit.SdfWriteErrorKind attribute) SGroupBracket (class in cosmolkit) SGroupCState (class in cosmolkit) SGroupDisplay (class in cosmolkit) SGroupPropertyKind (cosmolkit.MolPostErrorKind attribute) SGROUPS (cosmolkit.CxSmilesFields attribute) Shape (cosmolkit.CoordinateInputErrorKind attribute) sheet (cosmolkit.PdbReaderCause property) Sheet (cosmolkit.PdbReaderCauseKind attribute) Sheets (cosmolkit.BioMmcifReadStage attribute) sheets (cosmolkit.BioStructure attribute) (cosmolkit.BioStructureParts attribute) shells (cosmolkit.BioExperimentInfo attribute) ShortAtomCodes (cosmolkit.TopologicalTorsionPathScoreErrorKind attribute) SHORTCUT_LABELS (cosmolkit.AvalonFingerprintFlags attribute) ShortPath (cosmolkit.TopologicalTorsionPathScoreErrorKind attribute) show_warnings (cosmolkit.RemoveHsParams attribute) SI (cosmolkit.Element attribute) SIA (cosmolkit.ResidueCode attribute) side (cosmolkit.McsError property) (cosmolkit.SearchMcsError property) (cosmolkit.SmartsWriteError property) (cosmolkit.SubstructMatchError property) Sifts (cosmolkit.MmcifEntityInfoErrorKind attribute) sifts_unp (cosmolkit.BioResidue attribute) (cosmolkit.BioResidueRow attribute) sifts_unp_accessions (cosmolkit.BioEntityRow attribute) SiftsUnp (cosmolkit.BioMmcifReadStage attribute) sign (cosmolkit.PdbChargeError attribute) SignedTextOverflow (cosmolkit.PropertyIntReadErrorKind attribute) silent (cosmolkit.ReactionValidationParams attribute) SIMILARITY (cosmolkit.AvalonFingerprintFlags attribute) Simple (cosmolkit.AromaticityModel attribute) SINGLE (cosmolkit.BondOrder attribute) Single (cosmolkit.BondOrder attribute) (cosmolkit.MoleculeOpOutput attribute) (cosmolkit.UffPreparedOptimizationErrorKind attribute) SingleConformerOptimizationError SingleConformerOptimizationErrorKind (class in cosmolkit) SingleModelNumberUnavailable (cosmolkit.PdbCisPepRecordErrorKind attribute) site (cosmolkit.FingerprintError property) size (cosmolkit.FingerprintError property) skip_cleanup (cosmolkit.SmartsParseParams attribute) (cosmolkit.SmilesParseParams attribute) skip_queries (cosmolkit.AddHsParams attribute) skip_remarks (cosmolkit.BioPdbReadParams attribute) slogp_vsa() (cosmolkit.Molecule method) slogp_vsa_1() (cosmolkit.Molecule method) slogp_vsa_10() (cosmolkit.Molecule method) slogp_vsa_11() (cosmolkit.Molecule method) slogp_vsa_12() (cosmolkit.Molecule method) slogp_vsa_2() (cosmolkit.Molecule method) slogp_vsa_3() (cosmolkit.Molecule method) slogp_vsa_4() (cosmolkit.Molecule method) slogp_vsa_5() (cosmolkit.Molecule method) slogp_vsa_6() (cosmolkit.Molecule method) slogp_vsa_7() (cosmolkit.Molecule method) slogp_vsa_8() (cosmolkit.Molecule method) slogp_vsa_9() (cosmolkit.Molecule method) slogp_vsa_with_params() (cosmolkit.Molecule method) SlowFullCopy (cosmolkit.OrderedFragmentBuildErrorKind attribute) SM (cosmolkit.Element attribute) SmallestRingSize (cosmolkit.AtomQueryPredicateKind attribute) SmallestRingSizeGreaterEqual (cosmolkit.AtomQueryPredicateKind attribute) SmallestRingSizeLessEqual (cosmolkit.AtomQueryPredicateKind attribute) smarts (cosmolkit.CrystalffTorsionPreferencesError property) Smarts (cosmolkit.MaccsFingerprintErrorKind attribute) smarts (cosmolkit.McsResult attribute) Smarts (cosmolkit.PatternFingerprintErrorKind attribute) (cosmolkit.ReactionParseErrorKind attribute) smarts (cosmolkit.TautomerScoreTerm attribute) (cosmolkit.TautomerTransformError property) (cosmolkit.UffTorsionBondQueryError property) SmartsParse (cosmolkit.MorganErrorKind attribute) SmartsParseError SmartsParseErrorKind (class in cosmolkit) SmartsParseParams (class in cosmolkit) SmartsTraversalError SmartsTraversalErrorKind (class in cosmolkit) SmartsWrite (cosmolkit.MorganErrorKind attribute) SmartsWriteError SmartsWriteErrorKind (class in cosmolkit) SmartsWriteParams (class in cosmolkit) SMC (cosmolkit.ResidueCode attribute) SME (cosmolkit.ResidueCode attribute) smiles (cosmolkit.CxSmilesWriteParams attribute) (cosmolkit.FragmentSmilesWriteParams attribute) Smiles (cosmolkit.ReactionParseErrorKind attribute) smiles (cosmolkit.TautomerRunError property) Smiles (cosmolkit.TautomerRunErrorKind attribute) smiles_write (cosmolkit.EnumerationError property) SmilesError SmilesErrorKind (class in cosmolkit) SmilesParseError SmilesParseErrorKind (class in cosmolkit) SmilesParseParams (class in cosmolkit) SmilesStereoError SmilesStereoErrorKind (class in cosmolkit) SmilesWrite (cosmolkit.EnumerationErrorKind attribute) SmilesWriteError SmilesWriteErrorKind (class in cosmolkit) SmilesWriteParams (class in cosmolkit) smr_vsa() (cosmolkit.Molecule method) smr_vsa_1() (cosmolkit.Molecule method) smr_vsa_10() (cosmolkit.Molecule method) smr_vsa_2() (cosmolkit.Molecule method) smr_vsa_3() (cosmolkit.Molecule method) smr_vsa_4() (cosmolkit.Molecule method) smr_vsa_5() (cosmolkit.Molecule method) smr_vsa_6() (cosmolkit.Molecule method) smr_vsa_7() (cosmolkit.Molecule method) smr_vsa_8() (cosmolkit.Molecule method) smr_vsa_9() (cosmolkit.Molecule method) smr_vsa_with_params() (cosmolkit.Molecule method) SN (cosmolkit.Element attribute) snapshot() (cosmolkit.TautomerMoleculeView method) (cosmolkit.TautomerProgress method) SNC (cosmolkit.ResidueCode attribute) SNN (cosmolkit.ResidueCode attribute) SO4 (cosmolkit.ResidueCode attribute) software (cosmolkit.BioMetadata attribute) Software (cosmolkit.BioMmcifReadStage attribute) software (cosmolkit.BioMmcifWriteParams attribute) (cosmolkit.PdbRemark200Error attribute) Software (cosmolkit.PdbRemark200ErrorKind attribute) software_determined (cosmolkit.BioAssembly attribute) software_name (cosmolkit.BioAssembly attribute) solved_by (cosmolkit.BioMetadata attribute) solvent_free_energy_change (cosmolkit.BioAssembly attribute) SomethingUnexpected (cosmolkit.CipLabelerErrorKind attribute) SOR (cosmolkit.ResidueCode attribute) source (cosmolkit.AdjustHsError property) (cosmolkit.AlignmentError property) (cosmolkit.AromaticityError property) (cosmolkit.AtomCodeError property) (cosmolkit.AtomPairError property) (cosmolkit.AtomPairReadError property) (cosmolkit.AtomPathSubsetCopyError property) (cosmolkit.AtropisomerError property) (cosmolkit.AttachmentExpansionError property) (cosmolkit.AutomaticForceFieldConstructionError property) (cosmolkit.AvalonFingerprintError property) (cosmolkit.BatchError property) (cosmolkit.BatchImageError property) (cosmolkit.BioAtom attribute) (cosmolkit.BioAtomRow attribute) (cosmolkit.BioChain attribute) (cosmolkit.BioChainRow attribute) (cosmolkit.BioDiffractionInfo attribute) (cosmolkit.BioEntityRow attribute) (cosmolkit.BioMmcifReadError property) (cosmolkit.BioMmcifWriteError property) (cosmolkit.BioMoleculeConversionError property) (cosmolkit.BioMoleculeError property) (cosmolkit.BioOperationError property) (cosmolkit.BioPdbReadError property) (cosmolkit.BioPdbWriteError property) (cosmolkit.BioReadError property) (cosmolkit.BioResidue attribute) (cosmolkit.BioResidueRow attribute) (cosmolkit.BioRowTraverseError property) (cosmolkit.BioSelectionCopyCause property) (cosmolkit.BioSelectionCopyError property) (cosmolkit.BioSelectionMatchError property) (cosmolkit.BondDirectionStereoError property) (cosmolkit.BoundsQueryError property) (cosmolkit.CanonicalRankError property) (cosmolkit.ChemCompAtomError property) (cosmolkit.ChemCompModelError property) (cosmolkit.ChemistryProblemError property) (cosmolkit.CifReadError property) (cosmolkit.CipLabelerError property) (cosmolkit.CipRankError property) (cosmolkit.CleanupError property) (cosmolkit.ConformerOptimizerError property) (cosmolkit.ConformerRunError property) (cosmolkit.ConjugationError property) (cosmolkit.Coordinate2DError property) (cosmolkit.Coordinate2DLayoutError property) (cosmolkit.Coordinate2DTemplateError property) (cosmolkit.CoordinateBlockSelectionError property) (cosmolkit.CrystalffTorsionPreferencesError property) (cosmolkit.CxQueryLoweringError property) (cosmolkit.CxStereoGroupMergeError property) (cosmolkit.DescriptorError property) (cosmolkit.DescriptorReadError property) (cosmolkit.DescriptorSearchCause property) (cosmolkit.DispatchedUffOptimizationError property) (cosmolkit.DoubleBondStereoError property) (cosmolkit.DrawingError property) (cosmolkit.DrawingWriteError property) (cosmolkit.EnumerationError property) (cosmolkit.EnumerationRunError property) (cosmolkit.ExternalError property) (cosmolkit.FingerprintJsonError property) (cosmolkit.FingerprintPreparationError property) (cosmolkit.FingerprintWorkerError property) (cosmolkit.ForceFieldConstructionError property) (cosmolkit.ForceFieldError property) (cosmolkit.FragmentWriteInputError property) (cosmolkit.FullCopyComponentError property) (cosmolkit.GenerationError property) (cosmolkit.GenerationFailure property) (cosmolkit.GraphBoundsError property) (cosmolkit.HybridizationError property) (cosmolkit.HydrogenError property) (cosmolkit.IoError property) (cosmolkit.KekulizeError property) (cosmolkit.LayeredFingerprintError property) (cosmolkit.LegacyStereoError property) (cosmolkit.MaccsFingerprintError property) (cosmolkit.MatchError property) (cosmolkit.MatrixError property) (cosmolkit.McsError property) (cosmolkit.MissingExplicitHydrogensError property) (cosmolkit.MmcifAssemblyError property) (cosmolkit.MmcifAtomSiteGroupingError property) (cosmolkit.MmcifAtomSiteScalarError property) (cosmolkit.MmcifCcdRestoreError property) (cosmolkit.MmcifCisPepError property) (cosmolkit.MmcifConnectionError property) (cosmolkit.MmcifCrystalInfoError property) (cosmolkit.MmcifEntityInfoError property) (cosmolkit.MmcifHelixError property) (cosmolkit.MmcifLabelAddressError property) (cosmolkit.MmcifModResError property) (cosmolkit.MmcifSequenceIdError property) (cosmolkit.MmcifSheetError property) (cosmolkit.MmcifSiftsUnpError property) (cosmolkit.MmcifTlsInfoError property) (cosmolkit.MmffBuilderError property) (cosmolkit.MmffForceFieldError property) (cosmolkit.MmffMolPropertiesError property) (cosmolkit.MmffOptimizationError property) (cosmolkit.MmffOptimizationFailure property) (cosmolkit.MmffOptimizationSourceError property) (cosmolkit.MmffParamError property) (cosmolkit.MmffVdwParseError property) (cosmolkit.MmjsonReadError property) (cosmolkit.MmjsonStructureError property) (cosmolkit.Mol2PostError property) (cosmolkit.Mol2ReadError property) (cosmolkit.MolecularIoError property) (cosmolkit.MoleculeFragmentsError property) (cosmolkit.MoleculeFragmentsFailure property) (cosmolkit.MoleculeHashError property) (cosmolkit.MoleculeTransferError property) (cosmolkit.MolPostError property) (cosmolkit.MolProcessingError property) (cosmolkit.MolWriteError property) (cosmolkit.MorganError property) (cosmolkit.MorganReadError property) (cosmolkit.NonbondedAssemblyError property) (cosmolkit.NonbondedFragmentMappingError property) (cosmolkit.OperationError property) (cosmolkit.OptimizationStageError property) (cosmolkit.OrderedFragmentBuildError property) (cosmolkit.ParserCarrierError property) (cosmolkit.PathError property) (cosmolkit.PatternFingerprintError property) (cosmolkit.PdbCisPepRecordError attribute) (cosmolkit.PdbInputFormatError property) (cosmolkit.PdbLinkRecordError attribute) (cosmolkit.PdbModelTransitionError property) (cosmolkit.PdbPostprocessError property) (cosmolkit.PdbSheetError attribute) (cosmolkit.PdbSsbondRecordError attribute) (cosmolkit.PdbWriteError property) (cosmolkit.PickleError property) (cosmolkit.PotentialStereoError property) (cosmolkit.PropertyCacheError property) (cosmolkit.PropertyIntReadError property) (cosmolkit.PropertyUIntReadError property) (cosmolkit.PropertyULongReadError property) (cosmolkit.ProteinChainRef attribute) (cosmolkit.ProteinProjectionError property) (cosmolkit.ProteinReadError property) (cosmolkit.PruningError property) (cosmolkit.QueryGraphError property) (cosmolkit.QueryMatchContextError property) (cosmolkit.QueryStateError property) (cosmolkit.RadicalError property) (cosmolkit.ReactionApplyError property) (cosmolkit.ReactionInitializationError property) (cosmolkit.ReactionModelError property) (cosmolkit.ReactionParseError property) (cosmolkit.ReactionProductError property) (cosmolkit.ReactionRunError property) (cosmolkit.ReactionValidationError property) (cosmolkit.ReactionWriteError property) (cosmolkit.RingFindingError property) (cosmolkit.SanitizeError property) (cosmolkit.ScaffoldError property) (cosmolkit.SdfError property) (cosmolkit.SdfReadError property) (cosmolkit.SdfWriteError property) (cosmolkit.SelectedBondCopyError property) (cosmolkit.SerdeJsonError property) (cosmolkit.SerialConformerOptimizationError property) (cosmolkit.SerialUffOptimizationError property) (cosmolkit.SingleConformerOptimizationError property) (cosmolkit.SmartsParseError property) (cosmolkit.SmartsTraversalError property) (cosmolkit.SmartsWriteError property) (cosmolkit.SmilesError property) (cosmolkit.SmilesParseError property) (cosmolkit.SmilesStereoError property) (cosmolkit.SmilesWriteError property) (cosmolkit.StereoError property) (cosmolkit.StereoOrderError property) (cosmolkit.StereoReadError property) (cosmolkit.SubstructMatchError property) (cosmolkit.TautomerCatalogError property) (cosmolkit.TautomerRunError property) (cosmolkit.TautomerTransformError property) (cosmolkit.ThreadCountError property) (cosmolkit.ThreadSelectionError property) (cosmolkit.TopologicalFingerprintError property) (cosmolkit.TopologicalTorsionError property) (cosmolkit.TopologicalTorsionPathScoreError property) (cosmolkit.TopologicalTorsionReadError property) (cosmolkit.TopologyEditError property) (cosmolkit.TopologyValidationError property) (cosmolkit.TransformError property) (cosmolkit.UffBoundsError property) (cosmolkit.UffBuilderError property) (cosmolkit.UffConformerError property) (cosmolkit.UffDefaultTorsionQueryError property) (cosmolkit.UffEvaluationError property) (cosmolkit.UffForceFieldError property) (cosmolkit.UffOptimizationError property) (cosmolkit.UffParameterError property) (cosmolkit.UffParameterQueryError property) (cosmolkit.UffPreparedOptimizationError property) (cosmolkit.UffSingleError property) (cosmolkit.UffTorsionBondQueryError property) (cosmolkit.UffTypingError property) (cosmolkit.UnsignedStreamArrayError property) (cosmolkit.ValenceError property) (cosmolkit.WedgeError property) (cosmolkit.XyzReadError property) (cosmolkit.XyzWriteError property) source_atom (cosmolkit.SelectedSubstanceGroupCopyError property) source_bond (cosmolkit.SelectedSubstanceGroupCopyError property) source_code (cosmolkit.ResidueSequenceError property) source_conformer_order (cosmolkit.CoordinateBlock attribute) source_coordinate_dim (cosmolkit.CoordinateBlock attribute) (cosmolkit.SdfRecord attribute) source_entity_id (cosmolkit.EntitySourceIds attribute) source_message (cosmolkit.AdjacencyError property) (cosmolkit.AdjustHsError property) (cosmolkit.AlignmentError property) (cosmolkit.AromaticityError property) (cosmolkit.AtomCodeError property) (cosmolkit.AtomCodeExplanationError property) (cosmolkit.AtomPairError property) (cosmolkit.AtomPairReadError property) (cosmolkit.AtomPathSubsetCopyError property) (cosmolkit.AtomPropertyError property) (cosmolkit.AtomPropertyReadError property) (cosmolkit.AtropisomerError property) (cosmolkit.AttachmentExpansionError property) (cosmolkit.AutomaticForceFieldConstructionError property) (cosmolkit.AvalonFingerprintError property) (cosmolkit.BatchFingerprintOutputError property) (cosmolkit.BatchImageError property) (cosmolkit.BioMoleculeConversionError property) (cosmolkit.BioMoleculeError property) (cosmolkit.BioReadError property) (cosmolkit.BioRowChainError property) (cosmolkit.BioRowModelError property) (cosmolkit.BioRowTraverseError property) (cosmolkit.BioSelectionCopyCause property) (cosmolkit.BioStructureError property) (cosmolkit.BondDirectionStereoError property) (cosmolkit.BondValueError property) (cosmolkit.BoundsMatrixError property) (cosmolkit.BoundsQueryError property) (cosmolkit.CanonicalRankError property) (cosmolkit.ChemCompAtomError property) (cosmolkit.ChemCompModelError property) (cosmolkit.ChemistryProblemError property) (cosmolkit.CipLabelerError property) (cosmolkit.CipRankError property) (cosmolkit.CleanupError property) (cosmolkit.ConjugationError property) (cosmolkit.Coordinate2DError property) (cosmolkit.Coordinate2DLayoutError property) (cosmolkit.Coordinate2DTemplateError property) (cosmolkit.Coordinate3DReadError property) (cosmolkit.CoordinateBlockSelectionError property) (cosmolkit.CoordinateInputError property) (cosmolkit.CoordinateValidationError property) (cosmolkit.CrystalffTorsionPreferencesError property) (cosmolkit.CxQueryLoweringError property) (cosmolkit.CxStereoGroupMergeError property) (cosmolkit.DescriptorError property) (cosmolkit.DescriptorReadError property) (cosmolkit.DescriptorSearchCause property) (cosmolkit.DispatchedUffOptimizationError property) (cosmolkit.DoubleBondStereoError property) (cosmolkit.DrawingError property) (cosmolkit.DrawingWriteError property) (cosmolkit.EmbedFailureCountError property) (cosmolkit.EmbedSeedError property) (cosmolkit.EnumerationError property) (cosmolkit.FingerprintBatchError property) (cosmolkit.FingerprintError property) (cosmolkit.FingerprintPreparationError property) (cosmolkit.FingerprintWorkerError property) (cosmolkit.ForceFieldConstructionError property) (cosmolkit.ForceFieldKernelError property) (cosmolkit.FragmentCoordinateViewError property) (cosmolkit.FragmentWriteInputError property) (cosmolkit.FullCopyComponentError property) (cosmolkit.GenerationError property) (cosmolkit.GenerationFailure property) (cosmolkit.GraphBoundsError property) (cosmolkit.HybridizationError property) (cosmolkit.HydrogenError property) (cosmolkit.KekulizeError property) (cosmolkit.LayeredFingerprintError property) (cosmolkit.LegacyStereoError property) (cosmolkit.MaccsFingerprintError property) (cosmolkit.MappingValidationError property) (cosmolkit.MatchError property) (cosmolkit.MatrixError property) (cosmolkit.McsError property) (cosmolkit.McsProgressError property) (cosmolkit.MmcifAssemblyError property) (cosmolkit.MmcifAtomSiteGroupingError property) (cosmolkit.MmcifAtomSiteScalarError property) (cosmolkit.MmcifCcdRestoreError property) (cosmolkit.MmcifCisPepError property) (cosmolkit.MmcifConnectionError property) (cosmolkit.MmcifCrystalInfoError property) (cosmolkit.MmcifEntityInfoError property) (cosmolkit.MmcifHelixError property) (cosmolkit.MmcifLabelAddressError property) (cosmolkit.MmcifModResError property) (cosmolkit.MmcifOperationExprError property) (cosmolkit.MmcifSequenceIdError property) (cosmolkit.MmcifSheetError property) (cosmolkit.MmcifSiftsUnpError property) (cosmolkit.MmcifTlsInfoError property) (cosmolkit.MmffAngleLookupError property) (cosmolkit.MmffBuilderError property) (cosmolkit.MmffMolPropertiesError property) (cosmolkit.MmffOopLookupError property) (cosmolkit.MmffOptimizationFailure property) (cosmolkit.MmffParamError property) (cosmolkit.MmffTorLookupError property) (cosmolkit.MmffVdwParseError property) (cosmolkit.MmjsonReadError property) (cosmolkit.MmjsonStructureError property) (cosmolkit.MmjsonValueError property) (cosmolkit.Mol2ReadError property) (cosmolkit.MolecularIoError property) (cosmolkit.MoleculeFragmentsFailure property) (cosmolkit.MoleculeHashError property) (cosmolkit.MoleculePropertyError property) (cosmolkit.MoleculeTransferError property) (cosmolkit.MolPostError property) (cosmolkit.MolProcessingError property) (cosmolkit.MolWriteError property) (cosmolkit.MorganError property) (cosmolkit.MorganReadError property) (cosmolkit.NonbondedAssemblyError property) (cosmolkit.NonbondedFragmentMappingError property) (cosmolkit.OperationError property) (cosmolkit.OptimizationStageError property) (cosmolkit.OrderedFragmentBuildError property) (cosmolkit.ParserCarrierError property) (cosmolkit.ParserStereoOrderError property) (cosmolkit.PathError property) (cosmolkit.PatternFingerprintError property) (cosmolkit.PdbHeaderError property) (cosmolkit.PdbInputFormatError property) (cosmolkit.PdbModelTransitionError property) (cosmolkit.PdbPostprocessError property) (cosmolkit.PdbReaderCause property) (cosmolkit.PdbRemarkError property) (cosmolkit.PdbResidueKeyError property) (cosmolkit.PdbWriteError property) (cosmolkit.PickleError property) (cosmolkit.PotentialStereoError property) (cosmolkit.PropertyCacheError property) (cosmolkit.PropertyIntReadError property) (cosmolkit.PropertyUIntReadError property) (cosmolkit.PropertyULongReadError property) (cosmolkit.ProteinProjectionError property) (cosmolkit.ProteinReadError property) (cosmolkit.PruningError property) (cosmolkit.QueryAtomConversionError property) (cosmolkit.QueryGraphError property) (cosmolkit.QueryMatchContextError property) (cosmolkit.QueryStateError property) (cosmolkit.RadicalError property) (cosmolkit.ReactionApplyError property) (cosmolkit.ReactionInitializationError property) (cosmolkit.ReactionModelError property) (cosmolkit.ReactionParseError property) (cosmolkit.ReactionProductError property) (cosmolkit.ReactionRunError property) (cosmolkit.ReactionValidationError property) (cosmolkit.ReactionWriteError property) (cosmolkit.ResidueSequenceError property) (cosmolkit.RingDecomposerError property) (cosmolkit.RingFindingError property) (cosmolkit.SanitizeError property) (cosmolkit.ScaffoldError property) (cosmolkit.SdfError property) (cosmolkit.SdfReadError property) (cosmolkit.SdfWriteError property) (cosmolkit.SearchMcsError property) (cosmolkit.SelectedBondCopyError property) (cosmolkit.SelectedSubstanceGroupCopyError property) (cosmolkit.SerialConformerOptimizationError property) (cosmolkit.SerialUffOptimizationError property) (cosmolkit.SingleConformerOptimizationError property) (cosmolkit.SmartsParseError property) (cosmolkit.SmartsTraversalError property) (cosmolkit.SmartsWriteError property) (cosmolkit.SmilesError property) (cosmolkit.SmilesParseError property) (cosmolkit.SmilesStereoError property) (cosmolkit.SmilesWriteError property) (cosmolkit.StereoError property) (cosmolkit.StereoGroupError property) (cosmolkit.StereoOrderError property) (cosmolkit.StereoReadError property) (cosmolkit.SubstructMatchError property) (cosmolkit.SvgParseError property) (cosmolkit.TautomerRunError property) (cosmolkit.TautomerTransformError property) (cosmolkit.TopologicalFingerprintError property) (cosmolkit.TopologicalTorsionError property) (cosmolkit.TopologicalTorsionPathScoreError property) (cosmolkit.TopologicalTorsionReadError property) (cosmolkit.TopologyEditError property) (cosmolkit.TopologyValidationError property) (cosmolkit.TransformError property) (cosmolkit.UffBondMathError property) (cosmolkit.UffBuilderError property) (cosmolkit.UffDefaultTorsionQueryError property) (cosmolkit.UffInversionContributionError property) (cosmolkit.UffParamError property) (cosmolkit.UffParameterQueryError property) (cosmolkit.UffPreparedOptimizationError property) (cosmolkit.UffThreadCountError property) (cosmolkit.UffTorsionBondQueryError property) (cosmolkit.UffTypingError property) (cosmolkit.UIntLexicalReadError property) (cosmolkit.UnsignedStreamArrayError property) (cosmolkit.ValenceError property) (cosmolkit.WedgeError property) (cosmolkit.XyzReadError property) (cosmolkit.XyzWriteError property) source_model_number (cosmolkit.BioModel attribute) (cosmolkit.BioModelRow attribute) source_name (cosmolkit.BioReadError property) (cosmolkit.BioReadParams attribute) (cosmolkit.MmjsonReadError property) source_row (cosmolkit.FullCopyComponentError property) source_smarts (cosmolkit.RecursiveStructureQuery attribute) source_state (cosmolkit.BioStructure attribute) (cosmolkit.BioStructureParts attribute) source_text (cosmolkit.FullCopyComponentError property) (cosmolkit.ReactionApplyError property) source_type (cosmolkit.BioDiffractionInfo attribute) (cosmolkit.FingerprintJsonError property) source_uint (cosmolkit.FullCopyComponentError property) (cosmolkit.ReactionProductError property) SourceAngleIndexOverflow (cosmolkit.UffBuilderErrorKind attribute) SourceAtomCount (cosmolkit.SmartsWriteErrorKind attribute) SourceAtomToLeftIndex (cosmolkit.SmartsWriteErrorKind attribute) SourceBondBeginIndex (cosmolkit.SmartsWriteErrorKind attribute) SourceBondDirection (cosmolkit.SmartsWriteErrorKind attribute) SourceBondIndexOverflow (cosmolkit.UffBuilderErrorKind attribute) SourceCacheCommit (cosmolkit.TautomerRunErrorKind attribute) SourceConformerOrder (cosmolkit.CoordinateValidationErrorKind attribute) SourceDirectionVectorBelowTolerance (cosmolkit.UffBuilderErrorKind attribute) SourceGroupParentCycle (cosmolkit.TopologyEditErrorKind attribute) SourceIdNotRepresentable (cosmolkit.PdbStructureFinalizationErrorKind attribute) SourceIndexWidth (cosmolkit.WedgeErrorKind attribute) SourceIndexWidthExceeded (cosmolkit.CipLabelerErrorKind attribute) SourceIntegerOutsideDefinedRange (cosmolkit.PdbDbRefErrorKind attribute) SourceInversionIndexOverflow (cosmolkit.UffBuilderErrorKind attribute) SourceNumericStreamState (class in cosmolkit) SourcePort (cosmolkit.InchiErrorKind attribute) SourcePrecondition (cosmolkit.AtropisomerErrorKind attribute) (cosmolkit.WedgeErrorKind attribute) SourceRingFindType (cosmolkit.RingFindingErrorKind attribute) SourceSerialOutsideDefinedRange (cosmolkit.PdbConectErrorKind attribute) SourceSignedScoreOverflow (cosmolkit.WedgeErrorKind attribute) SourceStateIndex (cosmolkit.WedgeErrorKind attribute) SourceTbpAtomPrecondition (cosmolkit.UffBuilderErrorKind attribute) SourceTbpAxialBondNotFound (cosmolkit.UffBuilderErrorKind attribute) SourceTbpCenterParamsMissing (cosmolkit.UffBuilderErrorKind attribute) SourceTbpDegreePrecondition (cosmolkit.UffBuilderErrorKind attribute) SourceTbpEquatorialBondNotFound (cosmolkit.UffBuilderErrorKind attribute) SourceTbpHybridizationPrecondition (cosmolkit.UffBuilderErrorKind attribute) SourceText (cosmolkit.FullCopyComponentErrorKind attribute) (cosmolkit.ReactionApplyErrorKind attribute) SourceTorsionIndexOverflow (cosmolkit.UffBuilderErrorKind attribute) SourceUInt (cosmolkit.FullCopyComponentErrorKind attribute) (cosmolkit.ReactionProductErrorKind attribute) SourceUndefinedAccess (cosmolkit.PdbRemark350ErrorKind attribute) SourceUndefinedIntegerOverflow (cosmolkit.MmcifOperationExprErrorKind attribute) SourceUndefinedRangeIncrement (cosmolkit.MmcifOperationExprErrorKind attribute) SourceValenceOutOfRange (cosmolkit.UffBuilderErrorKind attribute) SourceValencePrecondition (cosmolkit.UffBuilderErrorKind attribute) SP (cosmolkit.Hybridization attribute) Sp (cosmolkit.Hybridization attribute) SP2 (cosmolkit.Hybridization attribute) Sp2 (cosmolkit.Hybridization attribute) SP2D (cosmolkit.Hybridization attribute) Sp2d (cosmolkit.Hybridization attribute) SP3 (cosmolkit.Hybridization attribute) Sp3 (cosmolkit.Hybridization attribute) SP3D (cosmolkit.Hybridization attribute) Sp3d (cosmolkit.Hybridization attribute) SP3D2 (cosmolkit.Hybridization attribute) Sp3d2 (cosmolkit.Hybridization attribute) space_group_hm (cosmolkit.BioCrystalInfo attribute) space_group_number (cosmolkit.BioCrystalInfo attribute) sparse_counts() (cosmolkit.MorganFingerprintGenerator method) (cosmolkit.TopologicalTorsionFingerprintGenerator method) sparse_fingerprints() (cosmolkit.MorganFingerprintGenerator method) (cosmolkit.TopologicalTorsionFingerprintGenerator method) SparseBitFingerprint (class in cosmolkit) SparseCountFingerprint (class in cosmolkit) SparseCountFingerprint32 (class in cosmolkit) SparseIndexOutOfRange (cosmolkit.FingerprintErrorKind attribute) SPD (cosmolkit.ResidueCode attribute) special_kind (cosmolkit.BioAssembly attribute) specified (cosmolkit.PotentialStereoInfo attribute) SPECIFIED (cosmolkit.PotentialStereoSpecified attribute) Specified (cosmolkit.PotentialStereoSpecified attribute) specified_stereo_query_matches_unspecified (cosmolkit.SubstructMatchParams attribute) SPK (cosmolkit.ResidueCode attribute) split_chain_on_ter (cosmolkit.BioPdbReadParams attribute) SPM (cosmolkit.ResidueCode attribute) SquarePlanar (cosmolkit.ChiralTag attribute) SR (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) sr_etkdg_v3() (cosmolkit.EmbedParams static method) ssbond_record (cosmolkit.PdbConnectionFinalizationError attribute) ssbond_resolution (cosmolkit.PdbConnectionFinalizationError attribute) SsbondRecord (cosmolkit.PdbConnectionFinalizationErrorKind attribute) SsbondResolution (cosmolkit.PdbConnectionFinalizationErrorKind attribute) stage (cosmolkit.BioMmcifReadError property) (cosmolkit.BioPdbReadError property) (cosmolkit.HydrogenError property) (cosmolkit.MmcifCrystalInfoError property) (cosmolkit.MmcifSiftsUnpError property) (cosmolkit.MmffOptimizationFailure property) Stage (cosmolkit.MmffOptimizationFailureKind attribute) stage (cosmolkit.Mol2PostError property) (cosmolkit.ReactionProductError property) (cosmolkit.SanitizeError property) StagingInvariant (cosmolkit.MmcifCrystalInfoErrorKind attribute) (cosmolkit.MmcifSiftsUnpErrorKind attribute) StagingRowOrder (cosmolkit.PdbStructureFinalizationErrorKind attribute) StaleNetworkFileHandle (cosmolkit.IoErrorKind attribute) STANDARD_RESIDUE_BOND_ORDERS (cosmolkit.PdbReadFlags attribute) start (cosmolkit.BioHelix attribute) (cosmolkit.BioRowSpan attribute) (cosmolkit.BioStrand attribute) (cosmolkit.BioStructureError property) (cosmolkit.MmjsonValueError property) (cosmolkit.ReactionParseError property) start_atom (cosmolkit.ReactionParseError property) start_bond (cosmolkit.ReactionParseError property) starting_model (cosmolkit.BioMetadata attribute) state (cosmolkit.DoubleLexicalReadError property) (cosmolkit.HydrogenError property) (cosmolkit.McsError property) State (cosmolkit.McsErrorKind attribute) state (cosmolkit.OperationError property) (cosmolkit.SmilesParseError property) (cosmolkit.WedgeError property) StateInvariantLost (cosmolkit.PdbRemark350ErrorKind attribute) StatePoisoned (cosmolkit.MorganErrorKind attribute) (cosmolkit.TopologicalTorsionErrorKind attribute) StateRows (cosmolkit.DrawingErrorKind attribute) states (cosmolkit.OperationError property) status (cosmolkit.MoleculeOpSpec attribute) (cosmolkit.OptimizationOutcome attribute) (cosmolkit.TautomerEnumeration attribute) (cosmolkit.TautomerProgress attribute) status_code (cosmolkit.MmffOptimizeMoleculeConfResult attribute) (cosmolkit.MmffOptimizeMoleculeResult attribute) (cosmolkit.OptimizationOutcome attribute) (cosmolkit.UffConformerResult attribute) (cosmolkit.UffOptimizationResult attribute) Stbn (cosmolkit.MmffParamTable attribute) stereo (cosmolkit.AtropisomerError property) Stereo (cosmolkit.BioMoleculeConversionErrorKind attribute) stereo (cosmolkit.Bond attribute) Stereo (cosmolkit.BondQueryPredicateKind attribute) (cosmolkit.DescriptorErrorKind attribute) stereo (cosmolkit.DoubleBondStereoError property) (cosmolkit.EnumerationError property) Stereo (cosmolkit.EnumerationErrorKind attribute) (cosmolkit.FragmentWriteInputErrorKind attribute) stereo (cosmolkit.GenerationError property) Stereo (cosmolkit.GenerationErrorKind attribute) (cosmolkit.MolProcessingErrorKind attribute) stereo (cosmolkit.OperationError property) Stereo (cosmolkit.OperationErrorKind attribute) stereo (cosmolkit.PotentialStereoResult attribute) (cosmolkit.ScaffoldError property) Stereo (cosmolkit.ScaffoldErrorKind attribute) (cosmolkit.SelectedBondCopyErrorKind attribute) (cosmolkit.SmartsTraversalErrorKind attribute) (cosmolkit.SmilesErrorKind attribute) stereo (cosmolkit.TopologyValidationError property) stereo_atoms (cosmolkit.Bond attribute) stereo_code (cosmolkit.Bond attribute) stereo_groups (cosmolkit.MoleculeBuilder attribute) stereo_name (cosmolkit.Bond attribute) stereo_order (cosmolkit.LegacyStereoError property) (cosmolkit.McsError property) (cosmolkit.ReactionProductError property) (cosmolkit.SubstructMatchError property) (cosmolkit.WedgeError property) stereo_type (cosmolkit.PotentialStereoInfo attribute) STEREOANY (cosmolkit.BondStereo attribute) StereoAssignment (cosmolkit.Coordinate2DErrorKind attribute) StereoAtomOutOfRange (cosmolkit.QueryGraphErrorKind attribute) (cosmolkit.TopologyValidationErrorKind attribute) StereoAtomsRequired (cosmolkit.BondValueErrorKind attribute) (cosmolkit.TopologyValidationErrorKind attribute) STEREOATROPCCW (cosmolkit.BondStereo attribute) STEREOATROPCW (cosmolkit.BondStereo attribute) StereoBond (cosmolkit.FragmentWriteInputErrorKind attribute) STEREOCIS (cosmolkit.BondStereo attribute) StereoDegreeArithmetic (cosmolkit.ReactionParseErrorKind attribute) STEREOE (cosmolkit.BondStereo attribute) StereoError StereoErrorKind (class in cosmolkit) StereoGetter (cosmolkit.ReactionProductErrorKind attribute) StereoGroup (class in cosmolkit) (cosmolkit.AtomPathSubsetCopyErrorKind attribute) (cosmolkit.AtropisomerErrorKind attribute) (cosmolkit.CanonicalRankErrorKind attribute) (cosmolkit.CxQueryLoweringErrorKind attribute) (cosmolkit.CxStereoGroupMergeErrorKind attribute) (cosmolkit.FragmentWriteInputErrorKind attribute) (cosmolkit.LegacyStereoErrorKind attribute) (cosmolkit.PathErrorKind attribute) (cosmolkit.PickleErrorKind attribute) (cosmolkit.QueryGraphErrorKind attribute) (cosmolkit.ReactionProductErrorKind attribute) (cosmolkit.SdfReadErrorKind attribute) (cosmolkit.SmartsParseErrorKind attribute) (cosmolkit.SmartsWriteErrorKind attribute) (cosmolkit.SmilesParseErrorKind attribute) (cosmolkit.StereoErrorKind attribute) (cosmolkit.TopologyEditErrorKind attribute) (cosmolkit.TopologyValidationErrorKind attribute) StereoGroupAtomOutOfRange (cosmolkit.AtropisomerErrorKind attribute) (cosmolkit.QueryGraphErrorKind attribute) (cosmolkit.TopologyValidationErrorKind attribute) StereoGroupBondOutOfRange (cosmolkit.AtropisomerErrorKind attribute) (cosmolkit.QueryGraphErrorKind attribute) (cosmolkit.TopologyValidationErrorKind attribute) StereoGroupError StereoGroupErrorKind (class in cosmolkit) StereoGroupKind (class in cosmolkit) StereoGroupMerge (cosmolkit.CxQueryLoweringErrorKind attribute) StereoInversionFlag (cosmolkit.ReactionParseErrorKind attribute) stereoisomer_count() (cosmolkit.Molecule method) stereoisomer_count_with_options() (cosmolkit.Molecule method) StereoisomerIterator (class in cosmolkit) StereoisomerOptions (class in cosmolkit) StereoisomerRandomSource (class in cosmolkit) STEREONONE (cosmolkit.BondStereo attribute) StereoOrder (cosmolkit.HydrogenErrorKind attribute) (cosmolkit.LegacyStereoErrorKind attribute) (cosmolkit.McsErrorKind attribute) (cosmolkit.PotentialStereoErrorKind attribute) (cosmolkit.ReactionParseErrorKind attribute) (cosmolkit.ReactionProductErrorKind attribute) (cosmolkit.StereoErrorKind attribute) (cosmolkit.SubstructMatchErrorKind attribute) (cosmolkit.WedgeErrorKind attribute) StereoOrderError StereoOrderErrorKind (class in cosmolkit) StereoReadError StereoReadErrorKind (class in cosmolkit) StereoReferenceIsOppositeEndpoint (cosmolkit.DoubleBondStereoErrorKind attribute) StereoReferenceNotNeighbor (cosmolkit.DoubleBondStereoErrorKind attribute) StereoReferenceOutOfRange (cosmolkit.TopologyValidationErrorKind attribute) StereoReferenceRequired (cosmolkit.DoubleBondStereoErrorKind attribute) STEREOTRANS (cosmolkit.BondStereo attribute) STEREOZ (cosmolkit.BondStereo attribute) storage_len (cosmolkit.UffBuilderError property) StorageFull (cosmolkit.IoErrorKind attribute) store_all (cosmolkit.McsParameters attribute) strands (cosmolkit.BioSheet attribute) Stream (cosmolkit.BioPdbReadStage attribute) Strict (cosmolkit.BatchErrorMode attribute) (cosmolkit.RotatableBondsOptions attribute) strict (cosmolkit.ValenceParams attribute) strict_cxsmiles (cosmolkit.ReactionParseParams attribute) (cosmolkit.SmartsParseParams attribute) (cosmolkit.SmilesParseParams attribute) strict_parsing (cosmolkit.SdfReadParams attribute) StrictLinkages (cosmolkit.RotatableBondsOptions attribute) String (cosmolkit.PropertyValueKind attribute) String() (cosmolkit.PropertyValue static method) StringTooLong (cosmolkit.PickleErrorKind attribute) StringVector (cosmolkit.PropertyValueKind attribute) StringVector() (cosmolkit.PropertyValue static method) struct_asym (cosmolkit.BioMmcifWriteParams attribute) struct_biol (cosmolkit.BioMmcifWriteParams attribute) struct_conf (cosmolkit.BioMmcifWriteParams attribute) struct_ref (cosmolkit.BioMmcifWriteParams attribute) struct_sheet (cosmolkit.BioMmcifWriteParams attribute) StructuralRepeatUnit (cosmolkit.SubstanceGroupKind attribute) Structure (cosmolkit.BioMmcifWriteErrorKind attribute) (cosmolkit.BioMoleculeConversionErrorKind attribute) (cosmolkit.BioOperationErrorKind attribute) (cosmolkit.BioSelectionCopyCauseKind attribute) (cosmolkit.MmjsonReadErrorKind attribute) (cosmolkit.PdbModelTransitionErrorKind attribute) structure (cosmolkit.PdbStructureFinalizationError attribute) Structure (cosmolkit.PdbStructureFinalizationErrorKind attribute) (cosmolkit.ProteinProjectionErrorKind attribute) (cosmolkit.ProteinReadErrorKind attribute) StructureTagParams (class in cosmolkit) StructureValidation (cosmolkit.BioMmcifReadStage attribute) subchain (cosmolkit.BioStructureError property) subchain_id (cosmolkit.ResidueSourceIds attribute) SubchainNotFound (cosmolkit.MmcifSiftsUnpErrorKind attribute) subchains (cosmolkit.BioAssemblyGenerator attribute) (cosmolkit.BioEntityRow attribute) substance_group (cosmolkit.SdfWriteError property) substance_group_copy (cosmolkit.AtomPathSubsetCopyError property) substance_groups (cosmolkit.MoleculeBuilder attribute) (cosmolkit.SdfRecord attribute) (cosmolkit.TopologyBlock attribute) SubstanceGroup (class in cosmolkit) (cosmolkit.SdfWriteErrorKind attribute) SubstanceGroupAtomList (class in cosmolkit) SubstanceGroupAtomOutOfRange (cosmolkit.QueryGraphErrorKind attribute) (cosmolkit.TopologyValidationErrorKind attribute) SubstanceGroupBondOutOfRange (cosmolkit.QueryGraphErrorKind attribute) (cosmolkit.TopologyValidationErrorKind attribute) SubstanceGroupCopy (cosmolkit.AtomPathSubsetCopyErrorKind attribute) SubstanceGroupId (class in cosmolkit) SubstanceGroupIdMismatch (cosmolkit.QueryGraphErrorKind attribute) (cosmolkit.TopologyValidationErrorKind attribute) SubstanceGroupKind (class in cosmolkit) SubstanceGroupParentOutOfRange (cosmolkit.QueryGraphErrorKind attribute) (cosmolkit.TopologyValidationErrorKind attribute) SubstituentsShouldBeTopologicallyEquivalent (cosmolkit.CipLabelerErrorKind attribute) substruct (cosmolkit.MatchError property) Substruct (cosmolkit.MatchErrorKind attribute) substruct_match() (cosmolkit.Molecule method) substruct_match_with_params() (cosmolkit.Molecule method) substruct_matches() (cosmolkit.Molecule method) substruct_matches_compiled() (cosmolkit.Molecule method) substruct_matches_with_params() (cosmolkit.Molecule method) SubstructMatch (cosmolkit.MorganErrorKind attribute) SubstructMatchError SubstructMatchErrorKind (class in cosmolkit) SubstructMatchParams (class in cosmolkit) SUBSTRUCTURE (cosmolkit.LayeredFingerprintLayers attribute) substructure (cosmolkit.TautomerScore attribute) subtract (cosmolkit.TopologicalTorsionPathScoreError property) SUC (cosmolkit.ResidueCode attribute) success (cosmolkit.BatchExportReport attribute) sum (cosmolkit.TransformError property) Superatom (cosmolkit.SubstanceGroupKind attribute) support_matrix() (in module cosmolkit) SupportMatrixEntry (class in cosmolkit) surface_area (cosmolkit.BioAssembly attribute) SvgParse (cosmolkit.DrawingErrorKind attribute) SvgParseError SvgParseErrorKind (class in cosmolkit) SvgTextProjection (cosmolkit.DrawingErrorKind attribute) SvgzFeatureNotEnabled (cosmolkit.SvgParseErrorKind attribute) symbol (cosmolkit.AtomCodeExplanation attribute) (cosmolkit.Element attribute) (cosmolkit.ElementInfo attribute) (cosmolkit.MmffParamError property) SYMM_RINGS (cosmolkit.SanitizeOperations attribute) symmetrize_conjugated_terminal_groups (cosmolkit.AllConformerRmsdParameters attribute) (cosmolkit.BestAlignmentParameters attribute) (cosmolkit.CoordinateRmsdParameters attribute) symmetrize_conjugated_terminal_groups_for_pruning (cosmolkit.EmbedParams attribute) symmetrized_sssr() (cosmolkit.Molecule method) symmetrized_sssr_with_params() (cosmolkit.Molecule method) symmetry (cosmolkit.BioMmcifWriteParams attribute) symmetry_images (cosmolkit.BioCrystalInfo attribute) SymmetryOperatorNotRepresentable (cosmolkit.MmcifConnectionErrorKind attribute) SymmetryOperatorOutsideSourceDefinedRange (cosmolkit.MmcifConnectionErrorKind attribute) SymmRings (cosmolkit.SanitizeStage attribute) synchrotron (cosmolkit.BioDiffractionInfo attribute) Syntax (cosmolkit.BioSelectionParseErrorKind attribute) (cosmolkit.CifReadErrorKind attribute) (cosmolkit.DoubleLexicalReadErrorKind attribute) (cosmolkit.SerdeJsonCategory attribute) (cosmolkit.SmilesParseErrorKind attribute) T t (cosmolkit.BioTlsGroup attribute) TA (cosmolkit.Element attribute) table (cosmolkit.BioStructureError property) Table (cosmolkit.ChemCompModelErrorKind attribute) table (cosmolkit.MmffParamError property) Table (cosmolkit.MmffParamErrorKind attribute) table (cosmolkit.MmffParamParseError property) Table (cosmolkit.MmffVdwParseErrorKind attribute) table (cosmolkit.PdbStructureFinalizationError attribute) table_len (cosmolkit.BioStructureError property) tables (cosmolkit.McsError property) TableTooLarge (cosmolkit.BioStructureErrorKind attribute) tag (cosmolkit.CipLabelerError property) (cosmolkit.RingFindingError property) (cosmolkit.StereoOrderError property) (cosmolkit.WedgeError property) tanimoto() (cosmolkit.Fingerprint method) TAR (cosmolkit.ResidueCode attribute) target (cosmolkit.HydrogenError property) (cosmolkit.OperationError property) (cosmolkit.RingDecomposerError property) (cosmolkit.SdfPropertyList attribute) (cosmolkit.SdfReadError property) (cosmolkit.TemplateAttachment attribute) (cosmolkit.TemplateAttachmentOrderError property) target_count (cosmolkit.MappingValidationError property) target_density (cosmolkit.TopologicalFingerprintParams attribute) target_mapping (cosmolkit.SubstructMatchError property) TargetAtomMappingMissing (cosmolkit.SearchMcsErrorKind attribute) TargetOutOfRange (cosmolkit.TemplateAttachmentOrderErrorKind attribute) TargetRemoved (cosmolkit.TemplateAttachmentOrderErrorKind attribute) targets (cosmolkit.McsError property) TargetTableCount (cosmolkit.McsErrorKind attribute) TAU (cosmolkit.ResidueCode attribute) tautomer (cosmolkit.OperationError property) Tautomer (cosmolkit.OperationErrorKind attribute) tautomer_score() (cosmolkit.Molecule method) (cosmolkit.TautomerMoleculeView method) tautomer_score_with_params() (cosmolkit.Molecule method) TautomerCatalogError TautomerCatalogErrorKind (class in cosmolkit) TautomerEnumeration (class in cosmolkit) TautomerEnumerationStatus (class in cosmolkit) tautomeric (cosmolkit.PatternFingerprintParams attribute) TautomerMoleculeView (class in cosmolkit) TautomerParams (class in cosmolkit) TautomerProgress (class in cosmolkit) TautomerRunError TautomerRunErrorKind (class in cosmolkit) TautomerScore (class in cosmolkit) TautomerScoreParams (class in cosmolkit) TautomerScoreTerm (class in cosmolkit) TautomerTransformError TautomerTransformErrorKind (class in cosmolkit) TB (cosmolkit.Element attribute) TBU (cosmolkit.ResidueCode attribute) TC (cosmolkit.Element attribute) TE (cosmolkit.Element attribute) temperature (cosmolkit.BioDiffractionInfo attribute) template (cosmolkit.ReactionModelError property) Template (cosmolkit.ReactionModelErrorKind attribute) template (cosmolkit.ReactionParseError property) (cosmolkit.ReactionRunError property) (cosmolkit.ReactionValidationError property) (cosmolkit.ReactionValidationIssue attribute) (cosmolkit.ReactionWriteError property) Template (cosmolkit.ReactionWriteErrorKind attribute) template (cosmolkit.SmartsWriteError property) template_attachment_order (cosmolkit.Atom attribute) (cosmolkit.MoleculeAtom attribute) template_property (cosmolkit.ReactionProductError property) TemplateAtomBounds (cosmolkit.ReactionParseErrorKind attribute) TemplateAttachment (class in cosmolkit) TemplateAttachmentOrder (class in cosmolkit) (cosmolkit.QueryGraphErrorKind attribute) (cosmolkit.TopologyValidationErrorKind attribute) TemplateAttachmentOrderError TemplateAttachmentOrderErrorKind (class in cosmolkit) TemplateAttachmentRemap (cosmolkit.CanonicalRankErrorKind attribute) (cosmolkit.PathErrorKind attribute) (cosmolkit.SmartsParseErrorKind attribute) (cosmolkit.TopologyEditErrorKind attribute) TemplateIndex (cosmolkit.ReactionModelErrorKind attribute) TemplateLoading (cosmolkit.Coordinate2DErrorKind attribute) TemplateMatch (cosmolkit.Coordinate2DLayoutErrorKind attribute) TemplateProperty (cosmolkit.ReactionParseErrorKind attribute) (cosmolkit.ReactionProductErrorKind attribute) TEP (cosmolkit.ResidueCode attribute) TER (cosmolkit.PdbWriteFlags attribute) ter_ignores_type (cosmolkit.BioPdbWriteParams attribute) ter_records (cosmolkit.BioPdbWriteParams attribute) ter_status (cosmolkit.BioStructure attribute) (cosmolkit.BioStructureSourceState attribute) terminal (cosmolkit.PruningError property) Terminal (cosmolkit.PruningErrorKind attribute) TerminalGroupSymmetrization (cosmolkit.AlignmentErrorKind attribute) termination (cosmolkit.EmbedMoleculeResult attribute) (cosmolkit.EmbedMultipleConfsResult attribute) terms (cosmolkit.TautomerScoreParams attribute) Tetrahedral (cosmolkit.ChiralTag attribute) TETRAHEDRAL_CLOCKWISE (cosmolkit.PotentialStereoDescriptor attribute) TETRAHEDRAL_COUNTERCLOCKWISE (cosmolkit.PotentialStereoDescriptor attribute) tetrahedral_stereo() (cosmolkit.Molecule method) TetrahedralCcw (cosmolkit.ChiralTag attribute) TetrahedralClockwise (cosmolkit.PotentialStereoDescriptor attribute) TetrahedralConfigurationMustHave4Carriers (cosmolkit.CipLabelerErrorKind attribute) TetrahedralCounterclockwise (cosmolkit.PotentialStereoDescriptor attribute) TetrahedralCw (cosmolkit.ChiralTag attribute) TetrahedralStereo (class in cosmolkit) Text (cosmolkit.MmjsonStructureErrorKind attribute) text (cosmolkit.ReactionParseError property) (cosmolkit.SmilesParseError property) text_property (cosmolkit.ScaffoldError property) TextBoundaryNotUtf8 (cosmolkit.PdbRemarkMetadataErrorKind attribute) TextFieldNotUtf8 (cosmolkit.PdbCrystalErrorKind attribute) (cosmolkit.PdbHeaderErrorKind attribute) (cosmolkit.PdbModResErrorKind attribute) (cosmolkit.PdbMtrixErrorKind attribute) (cosmolkit.PdbRemarkErrorKind attribute) (cosmolkit.PdbSheetErrorKind attribute) TextNotUtf8 (cosmolkit.PdbRemark200ErrorKind attribute) (cosmolkit.PdbRemark350ErrorKind attribute) (cosmolkit.PdbRemark3ErrorKind attribute) TextProperty (cosmolkit.ScaffoldErrorKind attribute) TFP (cosmolkit.ResidueCode attribute) TH (cosmolkit.Element attribute) Third (cosmolkit.ForceFieldAngleIndexArgument attribute) (cosmolkit.ForceFieldTorsionIndexArgument attribute) (cosmolkit.UffInversionIndexArgument attribute) THR (cosmolkit.ResidueCode attribute) thread_count (cosmolkit.GenerationError property) thread_selection (cosmolkit.AlignmentError property) ThreadCount (cosmolkit.DispatchedUffOptimizationErrorKind attribute) (cosmolkit.FingerprintWorkerErrorKind attribute) (cosmolkit.GenerationErrorKind attribute) (cosmolkit.TopologicalTorsionErrorKind attribute) ThreadCountError ThreadCountErrorKind (class in cosmolkit) ThreadObservation (cosmolkit.DispatchedUffOptimizationErrorKind attribute) threads (cosmolkit.MmffOptimizationFailure property) Threads (cosmolkit.MmffOptimizationFailureKind attribute) ThreadSelection (cosmolkit.AlignmentErrorKind attribute) ThreadSelectionError ThreadSpawn (cosmolkit.FingerprintWorkerErrorKind attribute) (cosmolkit.TopologicalTorsionErrorKind attribute) three_d (cosmolkit.CoordinateValidationError property) (cosmolkit.MolWriteError property) (cosmolkit.PdbWriteError property) three_d() (cosmolkit.ReactionCoordinateSelection static method) three_d_count (cosmolkit.SmilesParseError property) THREEANDAHALF (cosmolkit.BondOrder attribute) ThreeAndHalf (cosmolkit.BondOrder attribute) THREECENTER (cosmolkit.BondOrder attribute) ThreeCenter (cosmolkit.BondOrder attribute) ThreeColumnsForbidden (cosmolkit.CoordinateInputErrorKind attribute) ThreeD (cosmolkit.CoordinateDimension attribute) ThreeD() (cosmolkit.CxCoordinateSelection static method) (cosmolkit.MolCoordinateSelection static method) ThreeDimensionalCoordinates (cosmolkit.Coordinate2DTemplateErrorKind attribute) threshold (cosmolkit.McsError property) (cosmolkit.McsParameters attribute) threshold_unmapped_atoms (cosmolkit.ReactionTemplateRemovalParams attribute) ThresholdAboveOne (cosmolkit.SearchMcsErrorKind attribute) ThresholdCountOutOfRange (cosmolkit.McsErrorKind attribute) TI (cosmolkit.Element attribute) TimedOut (cosmolkit.EmbedTermination attribute) (cosmolkit.IoErrorKind attribute) timeout (cosmolkit.EmbedParams attribute) (cosmolkit.McsParameters attribute) title (cosmolkit.SdfRecord attribute) (cosmolkit.SdfRecordMetadata attribute) title_keywords (cosmolkit.BioMmcifWriteParams attribute) TL (cosmolkit.Element attribute) TLA (cosmolkit.ResidueCode attribute) Tls (cosmolkit.BioMmcifReadStage attribute) tls (cosmolkit.BioMmcifWriteParams attribute) tls_group_id (cosmolkit.BioAtom attribute) (cosmolkit.BioAtomRow attribute) tls_groups (cosmolkit.BioRefinementInfo attribute) TlsChainIdNotRepresentable (cosmolkit.PdbRemark3ErrorKind attribute) TlsOutsideSourceDefinedRange (cosmolkit.MmcifAtomSiteScalarErrorKind attribute) TM (cosmolkit.Element attribute) TMA (cosmolkit.ResidueCode attribute) to (cosmolkit.RingDecomposerError property) to_binary() (cosmolkit.Molecule method) to_builder() (cosmolkit.Molecule method) to_cid() (cosmolkit.BioSelection method) to_cx_smarts() (cosmolkit.Molecule method) to_cx_smarts_with_params() (cosmolkit.Molecule method) to_cx_smiles() (cosmolkit.Molecule method) to_cx_smiles_with_params() (cosmolkit.Molecule method) to_cx_smirks() (cosmolkit.Reaction method) to_cx_smirks_with_params() (cosmolkit.Reaction method) to_fragment_cx_smiles() (cosmolkit.Molecule method) to_fragment_cx_smiles_with_params() (cosmolkit.Molecule method) to_fragment_smiles() (cosmolkit.Molecule method) to_fragment_smiles_with_params() (cosmolkit.Molecule method) to_inchi() (cosmolkit.Molecule method) to_inchi_key() (cosmolkit.Molecule method) to_inchi_key_with_params() (cosmolkit.Molecule method) to_inchi_result() (cosmolkit.Molecule method) to_inchi_result_with_params() (cosmolkit.Molecule method) to_inchi_with_params() (cosmolkit.Molecule method) to_json() (cosmolkit.AtomPairAtomInvariantsGenerator method) (cosmolkit.AtomPairGeneratorParams method) (cosmolkit.EmbedParams method) (cosmolkit.MorganFingerprintGenerator method) (cosmolkit.MorganGeneratorParams method) (cosmolkit.TopologicalTorsionFingerprintGenerator method) (cosmolkit.TopologicalTorsionGeneratorParams method) to_list() (cosmolkit.MoleculeBatch method) to_mmcif() (cosmolkit.BioStructure method) to_mmcif_with_params() (cosmolkit.BioStructure method) to_mol() (cosmolkit.Molecule method) (cosmolkit.SdfRecord method) to_mol_with_params() (cosmolkit.Molecule method) (cosmolkit.SdfRecord method) to_molecule() (cosmolkit.BioStructure method) (cosmolkit.Protein method) to_molecule_with_params() (cosmolkit.BioStructure method) (cosmolkit.Protein method) to_numpy() (cosmolkit.Fingerprint method) (cosmolkit.FingerprintBatch method) to_owned() (cosmolkit.TautomerMoleculeView method) (cosmolkit.TautomerProgress method) to_pdb() (cosmolkit.BioStructure method) (cosmolkit.Molecule method) to_pdb_with_params() (cosmolkit.BioStructure method) (cosmolkit.Molecule method) to_png() (cosmolkit.Molecule method) to_random_smiles() (cosmolkit.Molecule method) to_random_smiles_with_params() (cosmolkit.Molecule method) to_sdf() (cosmolkit.Molecule method) (cosmolkit.SdfRecord method) to_sdf_2d() (cosmolkit.Molecule method) to_sdf_2d_with_params() (cosmolkit.Molecule method) to_sdf_3d() (cosmolkit.Molecule method) to_sdf_3d_with_params() (cosmolkit.Molecule method) to_sdf_with_params() (cosmolkit.Molecule method) (cosmolkit.SdfRecord method) to_smarts() (cosmolkit.Molecule method) to_smarts_with_params() (cosmolkit.Molecule method) to_smiles() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) (cosmolkit.TautomerMoleculeView method) to_smiles_with_params() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) to_smirks() (cosmolkit.Reaction method) to_smirks_with_params() (cosmolkit.Reaction method) to_svg() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) to_svg_with_params() (cosmolkit.MoleculeBatch method) to_xyz() (cosmolkit.Molecule method) to_xyz_with_params() (cosmolkit.Molecule method) token (cosmolkit.CrystalffTorsionPreferencesError property) (cosmolkit.SmilesParseError property) (cosmolkit.TopologyEditError property) token_index (cosmolkit.TopologyEditError property) TooFewInputs (cosmolkit.SearchMcsErrorKind attribute) Toolkit (cosmolkit.InchiErrorKind attribute) TooManyAtoms (cosmolkit.PickleErrorKind attribute) TooManyBonds (cosmolkit.PickleErrorKind attribute) TooManyLigands (cosmolkit.StereoOrderErrorKind attribute) TooManyLinks (cosmolkit.IoErrorKind attribute) TooManyNeighbors (cosmolkit.CipRankErrorKind attribute) TooManyNewBonds (cosmolkit.McsErrorKind attribute) TooManyNodes (cosmolkit.CipLabelerErrorKind attribute) TooShort (cosmolkit.PdbAtomFieldErrorKind attribute) topological_torsion_correction (cosmolkit.AtomPairAtomInvariantsGenerator attribute) topological_torsion_ids() (cosmolkit.Molecule method) topological_torsion_ids_with_params() (cosmolkit.Molecule method) topological_torsion_path_score() (cosmolkit.Molecule method) TopologicalFingerprintError TopologicalFingerprintErrorKind (class in cosmolkit) TopologicalFingerprintOutput (class in cosmolkit) TopologicalFingerprintOutputRequest (class in cosmolkit) TopologicalFingerprintParams (class in cosmolkit) TopologicalFingerprintResult (class in cosmolkit) TopologicalTorsionCallParams (class in cosmolkit) TopologicalTorsionError TopologicalTorsionErrorKind (class in cosmolkit) TopologicalTorsionFingerprintGenerator (class in cosmolkit) TopologicalTorsionFingerprintParams (class in cosmolkit) TopologicalTorsionGeneratorParams (class in cosmolkit) TopologicalTorsionPathScoreError TopologicalTorsionPathScoreErrorKind (class in cosmolkit) TopologicalTorsionReadError TopologicalTorsionReadErrorKind (class in cosmolkit) TopologicalTorsionSettings (class in cosmolkit) topology (cosmolkit.AromaticityError property) Topology (cosmolkit.AtomPairErrorKind attribute) (cosmolkit.AttachmentExpansionErrorKind attribute) (cosmolkit.BioMoleculeConversionErrorKind attribute) topology (cosmolkit.BoundsQueryError property) Topology (cosmolkit.BoundsQueryErrorKind attribute) topology (cosmolkit.CipLabelerError property) (cosmolkit.CipRankError property) (cosmolkit.CleanupError property) (cosmolkit.ConjugationError property) Topology (cosmolkit.DrawingErrorKind attribute) topology (cosmolkit.EnumerationError property) Topology (cosmolkit.EnumerationErrorKind attribute) topology (cosmolkit.GenerationError property) Topology (cosmolkit.GenerationErrorKind attribute) topology (cosmolkit.HybridizationError property) (cosmolkit.HydrogenError property) (cosmolkit.KekulizeError property) Topology (cosmolkit.LayeredFingerprintErrorKind attribute) TOPOLOGY (cosmolkit.LayeredFingerprintLayers attribute) topology (cosmolkit.LegacyStereoError property) Topology (cosmolkit.MaccsFingerprintErrorKind attribute) topology (cosmolkit.MatrixError property) Topology (cosmolkit.Mol2ReadErrorKind attribute) topology (cosmolkit.Molecule attribute) Topology (cosmolkit.MolProcessingErrorKind attribute) topology (cosmolkit.MolWriteError property) Topology (cosmolkit.MolWriteErrorKind attribute) topology (cosmolkit.PathError property) Topology (cosmolkit.PatternFingerprintErrorKind attribute) (cosmolkit.PdbPostprocessErrorKind attribute) (cosmolkit.PdbWriteErrorKind attribute) topology (cosmolkit.RingFindingError property) (cosmolkit.ScaffoldError property) Topology (cosmolkit.ScaffoldErrorKind attribute) (cosmolkit.SdfReadErrorKind attribute) (cosmolkit.SdfWriteErrorKind attribute) topology (cosmolkit.StereoOrderError property) (cosmolkit.StereoReadError property) (cosmolkit.TautomerRunError property) Topology (cosmolkit.TautomerRunErrorKind attribute) (cosmolkit.TopologicalFingerprintErrorKind attribute) topology (cosmolkit.WedgeError property) Topology (cosmolkit.WedgeErrorKind attribute) (cosmolkit.XyzReadErrorKind attribute) (cosmolkit.XyzWriteErrorKind attribute) topology_atom_count (cosmolkit.AromaticityError property) topology_bond_count (cosmolkit.AromaticityError property) topology_bounds (cosmolkit.GenerationFailure property) topology_edit (cosmolkit.FullCopyComponentError property) (cosmolkit.HydrogenError property) (cosmolkit.ReactionProductError property) topology_validation (cosmolkit.AtomPathSubsetCopyError property) TopologyBlock (class in cosmolkit) TopologyBounds (cosmolkit.GenerationFailureKind attribute) TopologyEdit (cosmolkit.DescriptorErrorKind attribute) (cosmolkit.FullCopyComponentErrorKind attribute) (cosmolkit.HydrogenErrorKind attribute) (cosmolkit.MolProcessingErrorKind attribute) (cosmolkit.PdbPostprocessErrorKind attribute) (cosmolkit.ReactionProductErrorKind attribute) (cosmolkit.SmilesParseErrorKind attribute) TopologyEditError TopologyEditErrorKind (class in cosmolkit) TopologyValidation (cosmolkit.AtomPathSubsetCopyErrorKind attribute) (cosmolkit.UffBuilderErrorKind attribute) TopologyValidationError TopologyValidationErrorKind (class in cosmolkit) Tor (cosmolkit.MmffParamTable attribute) torsion (cosmolkit.MmffParamError property) Torsion (cosmolkit.MmffParamErrorKind attribute) torsion_atom_count (cosmolkit.LegacyTopologicalTorsionParams attribute) (cosmolkit.TopologicalTorsionFingerprintParams attribute) (cosmolkit.TopologicalTorsionGeneratorParams attribute) (cosmolkit.TopologicalTorsionSettings attribute) torsion_bond_query (cosmolkit.MmffBuilderError property) torsion_preferences (cosmolkit.GenerationFailure property) TorsionAddressOutsideDefinedSource (cosmolkit.ForceFieldKernelErrorKind attribute) TorsionBadHybridizations (cosmolkit.ForceFieldKernelErrorKind attribute) TorsionBadOrder (cosmolkit.ForceFieldKernelErrorKind attribute) TorsionBondQuery (cosmolkit.MmffBuilderErrorKind attribute) (cosmolkit.UffBuilderErrorKind attribute) TorsionBoundsOrder (cosmolkit.ForceFieldKernelErrorKind attribute) TorsionDegeneratePoints (cosmolkit.ForceFieldKernelErrorKind attribute) TorsionIndexOutOfRange (cosmolkit.ForceFieldKernelErrorKind attribute) TorsionParametersOutsideDefinedSource (cosmolkit.ForceFieldKernelErrorKind attribute) TorsionPreferences (cosmolkit.GenerationFailureKind attribute) total (cosmolkit.BatchExportReport attribute) (cosmolkit.TautomerScore attribute) total_atom_count() (cosmolkit.Molecule method) total_hydrogens (cosmolkit.AtomMetadata attribute) (cosmolkit.MoleculeAtom attribute) total_valence (cosmolkit.AtomMetadata attribute) (cosmolkit.MoleculeAtom attribute) total_value() (cosmolkit.SparseCountFingerprint method) (cosmolkit.SparseCountFingerprint32 method) TotalDegree (cosmolkit.AtomQueryPredicateKind attribute) (cosmolkit.AtomRangeDataFunctionKind attribute) TotalDegreeGreaterEqual (cosmolkit.AtomQueryPredicateKind attribute) TotalDegreeLessEqual (cosmolkit.AtomQueryPredicateKind attribute) TotalValence (cosmolkit.AtomQueryPredicateKind attribute) (cosmolkit.AtomRangeDataFunctionKind attribute) (cosmolkit.UffTypingInput attribute) TotalValenceGreaterEqual (cosmolkit.AtomQueryPredicateKind attribute) TotalValenceLessEqual (cosmolkit.AtomQueryPredicateKind attribute) TOX (cosmolkit.ResidueCode attribute) TPO (cosmolkit.ResidueCode attribute) TPQ (cosmolkit.ResidueCode attribute) tpsa() (cosmolkit.Molecule method) tpsa_with_params() (cosmolkit.Molecule method) track_failures (cosmolkit.EmbedParams attribute) TrackerCount (cosmolkit.CxStereoGroupMergeErrorKind attribute) TrackerPropertyType (cosmolkit.CxStereoGroupMergeErrorKind attribute) TrailingByte (cosmolkit.DoubleLexicalReadErrorKind attribute) TrailingEscape (cosmolkit.CrystalffTorsionPreferencesErrorKind attribute) Trans (cosmolkit.BondStereo attribute) TransferPostcondition (cosmolkit.ForceFieldKernelErrorKind attribute) transform (cosmolkit.AlignmentResult attribute) (cosmolkit.BioAssemblyOperator attribute) (cosmolkit.BioNcsOperator attribute) Transform (cosmolkit.MmcifAssemblyErrorKind attribute) transform (cosmolkit.OperationError property) Transform (cosmolkit.OperationErrorKind attribute) transform (cosmolkit.TautomerCatalogError property) Transform (cosmolkit.TautomerCatalogErrorKind attribute) transform_count (cosmolkit.TautomerParams attribute) TransformError TransformErrorKind (class in cosmolkit) TransformIndexOutOfRange (cosmolkit.TautomerCatalogErrorKind attribute) translate_() (cosmolkit.BioStructure method) (cosmolkit.Protein method) translation (cosmolkit.BioTransform attribute) Traversal (cosmolkit.SmartsTraversalErrorKind attribute) (cosmolkit.SmartsWriteErrorKind attribute) TraversalStateIndex (cosmolkit.SmilesParseErrorKind attribute) TraversalTooManyOpenRings (cosmolkit.SmilesParseErrorKind attribute) Traverse (cosmolkit.BioSelectionCopyCauseKind attribute) TRE (cosmolkit.ResidueCode attribute) TrigonalBipyramidal (cosmolkit.ChiralTag attribute) TRIPLE (cosmolkit.BondOrder attribute) Triple (cosmolkit.BondOrder attribute) TRP (cosmolkit.ResidueCode attribute) TRQ (cosmolkit.ResidueCode attribute) TRS (cosmolkit.ResidueCode attribute) TRT (cosmolkit.ResidueCode attribute) True_ (cosmolkit.MmjsonUnexpectedType attribute) try_embedding (cosmolkit.StereoisomerOptions attribute) TryReserveError TS (cosmolkit.Element attribute) two_d (cosmolkit.CoordinateValidationError property) (cosmolkit.MolWriteError property) (cosmolkit.PdbWriteError property) two_d() (cosmolkit.ReactionCoordinateSelection static method) two_d_count (cosmolkit.SmilesParseError property) TWOANDAHALF (cosmolkit.BondOrder attribute) TwoAndHalf (cosmolkit.BondOrder attribute) TwoD (cosmolkit.CoordinateDimension attribute) TwoD() (cosmolkit.CxCoordinateSelection static method) (cosmolkit.MolCoordinateSelection static method) Type (cosmolkit.AtomPropertyReadErrorKind attribute) type_name (cosmolkit.PickleError property) typed (cosmolkit.StereoOrderError property) Typing (cosmolkit.AutomaticForceFieldConstructionErrorKind attribute) (cosmolkit.UffParameterErrorKind attribute) TYR (cosmolkit.ResidueCode attribute) TYS (cosmolkit.ResidueCode attribute) U U (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) Uff (cosmolkit.GraphBoundsErrorKind attribute) uff_energy_gradient() (cosmolkit.Molecule method) uff_energy_gradient_with_params() (cosmolkit.Molecule method) uff_force_field() (cosmolkit.Molecule method) uff_has_all_molecule_params() (cosmolkit.Molecule method) uff_optimization (cosmolkit.OperationError property) UffBondMathError UffBondMathErrorKind (class in cosmolkit) UffBoundsCause (class in cosmolkit) UffBoundsCauseKind (class in cosmolkit) UffBoundsError UffBuilderError UffBuilderErrorKind (class in cosmolkit) UffConformerError UffConformerOptimizationParams (class in cosmolkit) UffConformerOptimizationResult (class in cosmolkit) UffConformerResult (class in cosmolkit) UffDefaultTorsionQueryError UffDefaultTorsionQueryErrorKind (class in cosmolkit) UffEnergyGradient (class in cosmolkit) UffEvaluationError UffEvaluationFailure (class in cosmolkit) UffEvaluationFailureKind (class in cosmolkit) UffEvaluationParams (class in cosmolkit) UffForceFieldError UffForceFieldParams (class in cosmolkit) UffInversionContributionError UffInversionContributionErrorKind (class in cosmolkit) UffInversionIndexArgument (class in cosmolkit) UffOptimization (cosmolkit.OperationErrorKind attribute) UffOptimizationError UffOptimizationErrorKind (class in cosmolkit) UffOptimizationParams (class in cosmolkit) UffOptimizationResult (class in cosmolkit) UffParamError UffParamErrorKind (class in cosmolkit) UffParameterError UffParameterErrorKind (class in cosmolkit) UffParameterQueryError UffParameterQueryErrorKind (class in cosmolkit) UffPreparedOptimizationError UffPreparedOptimizationErrorKind (class in cosmolkit) UffPreparedValenceField (class in cosmolkit) UffSingleError UffThreadCountError UffThreadCountErrorKind (class in cosmolkit) UffTorsionBondQueryError UffTorsionBondQueryErrorKind (class in cosmolkit) UffTypingError UffTypingErrorKind (class in cosmolkit) UffTypingInput (class in cosmolkit) UInt (cosmolkit.PropertyValueKind attribute) UInt() (cosmolkit.PropertyValue static method) uint_property (cosmolkit.ScaffoldError property) UIntLexicalReadError UIntLexicalReadErrorKind (class in cosmolkit) UIntProperty (cosmolkit.ScaffoldErrorKind attribute) UMQ (cosmolkit.ResidueCode attribute) UnbalancedRingClosure (cosmolkit.SmartsParseErrorKind attribute) UnclosedBracket (cosmolkit.SmartsParseErrorKind attribute) UnclosedParenthesis (cosmolkit.SmartsParseErrorKind attribute) UnclosedRing (cosmolkit.SmilesParseErrorKind attribute) UnclosedRootNode (cosmolkit.XmlParseErrorKind attribute) UndefinedArithmetic (cosmolkit.FingerprintErrorKind attribute) UndefinedGroupPdbIndex (cosmolkit.MmcifAtomSiteGroupingErrorKind attribute) UndefinedPhNumericScreening (cosmolkit.PdbRemark200ErrorKind attribute) UndefinedResolutionField (cosmolkit.PdbRemarkMetadataErrorKind attribute) UndefinedRotationAxis (cosmolkit.TransformErrorKind attribute) UndefinedSamplingDistance (cosmolkit.Coordinate2DLayoutErrorKind attribute) UndefinedSignedNegation (cosmolkit.ThreadCountErrorKind attribute) (cosmolkit.UffThreadCountErrorKind attribute) UndefinedStereo (cosmolkit.DoubleBondStereoErrorKind attribute) UnexpectedCharacter (cosmolkit.SmartsParseErrorKind attribute) UnexpectedCloseTag (cosmolkit.XmlParseErrorKind attribute) UnexpectedComma (cosmolkit.JsonErrorKind attribute) UnexpectedDeclaration (cosmolkit.XmlParseErrorKind attribute) UnexpectedEnd (cosmolkit.JsonErrorKind attribute) (cosmolkit.SmartsParseErrorKind attribute) UnexpectedEndOfStream (cosmolkit.XmlParseErrorKind attribute) UnexpectedEndOfUtf16 (cosmolkit.JsonErrorKind attribute) UnexpectedEntityCloseTag (cosmolkit.XmlParseErrorKind attribute) UnexpectedEof (cosmolkit.IoErrorKind attribute) (cosmolkit.PickleErrorKind attribute) (cosmolkit.XyzReadErrorKind attribute) UnexpectedLetter (cosmolkit.ResidueSequenceErrorKind attribute) UnexpectedTopologyShape (cosmolkit.AromaticityErrorKind attribute) UnexpectedType (cosmolkit.MmjsonValueErrorKind attribute) UnexpectedUpEdgeOrdering (cosmolkit.CipLabelerErrorKind attribute) UnexpectedXmlnsUri (cosmolkit.XmlParseErrorKind attribute) UnexpectedXmlUri (cosmolkit.XmlParseErrorKind attribute) UninitializedRecursiveQuery (cosmolkit.SubstructMatchErrorKind attribute) UninitializedRings (cosmolkit.QueryMatchContextErrorKind attribute) unique (cosmolkit.StereoisomerOptions attribute) unique_reflections (cosmolkit.BioExperimentInfo attribute) uniquify (cosmolkit.SubstructMatchParams attribute) UNK (cosmolkit.ResidueCode attribute) Unknown (cosmolkit.BioConnectionKind attribute) (cosmolkit.BioCoordinateFormat attribute) UNKNOWN (cosmolkit.BondDirection attribute) Unknown (cosmolkit.BondDirection attribute) (cosmolkit.ChainKind attribute) (cosmolkit.EntityKind attribute) (cosmolkit.PolymerKind attribute) UNKNOWN (cosmolkit.PotentialStereoSpecified attribute) Unknown (cosmolkit.PotentialStereoSpecified attribute) UNKNOWN (cosmolkit.ResidueCode attribute) (cosmolkit.ResidueInfoKind attribute) Unknown (cosmolkit.ResidueKind attribute) unknown_bits (cosmolkit.SanitizeError property) UnknownChirality (cosmolkit.AtomCodeExplanationErrorKind attribute) UnknownCombination (cosmolkit.SmartsWriteErrorKind attribute) UnknownEntityReference (cosmolkit.XmlParseErrorKind attribute) UnknownEscape (cosmolkit.JsonErrorKind attribute) UnknownFileFormat (cosmolkit.BioReadErrorKind attribute) UnknownHelix (cosmolkit.BioHelixClass attribute) UnknownIsotope (cosmolkit.PeriodicTableErrorKind attribute) UnknownNamespace (cosmolkit.XmlParseErrorKind attribute) UnknownRequiredSection (cosmolkit.PickleErrorKind attribute) UnknownStereoProperty (cosmolkit.StereoErrorKind attribute) UnknownToken (cosmolkit.XmlParseErrorKind attribute) UnknownZPolicy (cosmolkit.CoordinateInputErrorKind attribute) UnmappedProduct (cosmolkit.ReactionValidationIssueKind attribute) UnmappedReactant (cosmolkit.ReactionValidationIssueKind attribute) UnmappedReactantMaps (cosmolkit.ReactionValidationIssueKind attribute) UnmatchedParenthesis (cosmolkit.ResidueSequenceErrorKind attribute) UnrepresentableEndpoint (cosmolkit.BondEndPointsParseErrorKind attribute) UnrepresentableField (cosmolkit.BioPdbWriteErrorKind attribute) unsigned_property (cosmolkit.MolWriteError property) UnsignedOverflow (cosmolkit.PropertyIntReadErrorKind attribute) UnsignedProperty (cosmolkit.MolWriteErrorKind attribute) (cosmolkit.SdfWriteErrorKind attribute) UnsignedPropertyOverflow (cosmolkit.DoubleBondStereoErrorKind attribute) (cosmolkit.MolPostErrorKind attribute) (cosmolkit.SdfWriteErrorKind attribute) UnsignedPropertyRead (cosmolkit.CipLabelerErrorKind attribute) UnsignedRankOverflow (cosmolkit.CanonicalRankErrorKind attribute) (cosmolkit.WedgeErrorKind attribute) UnsignedStreamArrayError UnsignedStreamArrayErrorKind (class in cosmolkit) Unspecified (cosmolkit.BioSoftwareClassification attribute) UNSPECIFIED (cosmolkit.BondOrder attribute) Unspecified (cosmolkit.BondOrder attribute) (cosmolkit.ChiralTag attribute) UNSPECIFIED (cosmolkit.Hybridization attribute) Unspecified (cosmolkit.Hybridization attribute) UNSPECIFIED (cosmolkit.PotentialStereoSpecified attribute) Unspecified (cosmolkit.PotentialStereoSpecified attribute) Unsupported (cosmolkit.ConformerErrorKind attribute) (cosmolkit.DescriptorErrorKind attribute) (cosmolkit.FingerprintErrorKind attribute) (cosmolkit.HydrogenErrorKind attribute) (cosmolkit.IoErrorKind attribute) (cosmolkit.Mol2ReadErrorKind attribute) (cosmolkit.OperationErrorKind attribute) (cosmolkit.PdbPostprocessErrorKind attribute) (cosmolkit.PdbWriteErrorKind attribute) (cosmolkit.SdfReadErrorKind attribute) (cosmolkit.SmilesParseErrorKind attribute) (cosmolkit.SubstructMatchErrorKind attribute) unsupported_atom_predicate (cosmolkit.MatchError property) unsupported_bond_predicate (cosmolkit.MatchError property) unsupported_cx (cosmolkit.SmilesParseError property) unsupported_subset (cosmolkit.MolWriteError property) unsupported_writer (cosmolkit.SmilesParseError property) UnsupportedArchiveVersion (cosmolkit.PickleErrorKind attribute) UnsupportedAtomPredicate (cosmolkit.MatchErrorKind attribute) UnsupportedAtomQuery (cosmolkit.SmartsWriteErrorKind attribute) UnsupportedBondOrder (cosmolkit.CipRankErrorKind attribute) (cosmolkit.MatrixErrorKind attribute) (cosmolkit.PotentialStereoErrorKind attribute) UnsupportedBondPredicate (cosmolkit.MatchErrorKind attribute) UnsupportedBondQuery (cosmolkit.SmartsWriteErrorKind attribute) UnsupportedBranch (cosmolkit.RingFindingErrorKind attribute) UnsupportedCenterTag (cosmolkit.WedgeErrorKind attribute) UnsupportedComponent (cosmolkit.FingerprintJsonErrorKind attribute) UnsupportedConfiguration (cosmolkit.CipLabelerErrorKind attribute) UnsupportedCx (cosmolkit.SmilesParseErrorKind attribute) UnsupportedEscapeSequence (cosmolkit.CrystalffTorsionPreferencesErrorKind attribute) UnsupportedFeature (cosmolkit.AtomQueryPredicateKind attribute) (cosmolkit.BondQueryPredicateKind attribute) (cosmolkit.OperationErrorKind attribute) (cosmolkit.SmartsParseErrorKind attribute) UnsupportedFeatureError (class in cosmolkit) UnsupportedImplementation (cosmolkit.GenerationErrorKind attribute) UnsupportedKind (cosmolkit.PropertyStringErrorKind attribute) UnsupportedModel (cosmolkit.AromaticityErrorKind attribute) UnsupportedOption (cosmolkit.MaccsFingerprintErrorKind attribute) UnsupportedQueryState (cosmolkit.KekulizeErrorKind attribute) UnsupportedRecord (cosmolkit.CxQueryLoweringErrorKind attribute) UnsupportedSectionVersion (cosmolkit.PickleErrorKind attribute) UnsupportedState (cosmolkit.AromaticityErrorKind attribute) (cosmolkit.InchiErrorKind attribute) UnsupportedStereo (cosmolkit.DoubleBondStereoErrorKind attribute) UnsupportedSubset (cosmolkit.MolWriteErrorKind attribute) UnsupportedTetrahedralTag (cosmolkit.StereoOrderErrorKind attribute) UnsupportedVersion (cosmolkit.PickleErrorKind attribute) UnsupportedWriter (cosmolkit.SmilesParseErrorKind attribute) UnterminatedQuotedLiteral (cosmolkit.CrystalffTorsionPreferencesErrorKind attribute) UnwritableBondQuery (cosmolkit.SmartsWriteErrorKind attribute) update_explicit_count (cosmolkit.RemoveHsParams attribute) upper (cosmolkit.AtomRangeBounds attribute) (cosmolkit.AtomRangeDataFunction attribute) Upper (cosmolkit.BoundKind attribute) upper (cosmolkit.PathError property) upper_bound (cosmolkit.ForceFieldKernelError property) (cosmolkit.UffInversionContributionError property) upper_open (cosmolkit.AtomRangeBounds attribute) (cosmolkit.AtomRangeDataFunction attribute) UR3 (cosmolkit.ResidueCode attribute) URE (cosmolkit.ResidueCode attribute) use_2d (cosmolkit.AtomPairFingerprintParams attribute) (cosmolkit.AtomPairGeneratorParams attribute) use_atom_weights (cosmolkit.DistanceMatrix3dParams attribute) (cosmolkit.DistanceMatrixParams attribute) use_basic_knowledge (cosmolkit.EmbedParams attribute) use_bond_order (cosmolkit.DistanceMatrixParams attribute) (cosmolkit.TopologicalFingerprintParams attribute) use_bond_types (cosmolkit.MorganBondInvariantsGenerator attribute) (cosmolkit.MorganFingerprintParams attribute) (cosmolkit.MorganGeneratorParams attribute) use_chirality (cosmolkit.SubstructMatchParams attribute) use_enhanced_stereo (cosmolkit.SubstructMatchParams attribute) use_exp_torsion_angle_prefs (cosmolkit.EmbedParams attribute) use_generic_matchers (cosmolkit.SubstructMatchParams attribute) use_hs (cosmolkit.TopologicalFingerprintParams attribute) use_legacy_stereo_perception (cosmolkit.AtomPairFingerprintParams attribute) (cosmolkit.TopologicalTorsionCallParams attribute) (cosmolkit.TopologicalTorsionFingerprintParams attribute) use_macrocycle14config (cosmolkit.EmbedParams attribute) use_macrocycle_torsions (cosmolkit.EmbedParams attribute) use_path_angle_expansion (cosmolkit.Coordinate2DParams attribute) use_query_query_matches (cosmolkit.SubstructMatchParams attribute) use_random_coords (cosmolkit.EmbedParams attribute) use_ring_templates (cosmolkit.Coordinate2DParams attribute) use_small_ring_torsions (cosmolkit.EmbedParams attribute) use_smiles (cosmolkit.ReactionParseParams attribute) use_symmetry_for_pruning (cosmolkit.EmbedParams attribute) Utf8 (cosmolkit.AtomPropertyReadErrorKind attribute) (cosmolkit.BioReadErrorKind attribute) (cosmolkit.PdbStructureFinalizationErrorKind attribute) utf8_error (cosmolkit.FromUtf8Error property) Utf8Error V V (cosmolkit.Element attribute) v1() (cosmolkit.TautomerParams static method) V2000 (cosmolkit.SdfFormat attribute) V3000 (cosmolkit.SdfFormat attribute) VAL (cosmolkit.ResidueCode attribute) valence (cosmolkit.AdjustHsError property) Valence (cosmolkit.AdjustHsErrorKind attribute) valence (cosmolkit.AromaticityError property) Valence (cosmolkit.AromaticityErrorKind attribute) (cosmolkit.AtomCodeErrorKind attribute) (cosmolkit.AtropisomerErrorKind attribute) (cosmolkit.AttachmentExpansionErrorKind attribute) (cosmolkit.BioMoleculeConversionErrorKind attribute) valence (cosmolkit.BondDirectionStereoError property) Valence (cosmolkit.BondDirectionStereoErrorKind attribute) valence (cosmolkit.BoundsQueryError property) Valence (cosmolkit.BoundsQueryErrorKind attribute) valence (cosmolkit.CanonicalRankError property) Valence (cosmolkit.CanonicalRankErrorKind attribute) valence (cosmolkit.ChemistryProblemError property) Valence (cosmolkit.ChemistryProblemErrorKind attribute) valence (cosmolkit.CipLabelerError property) Valence (cosmolkit.CipLabelerErrorKind attribute) valence (cosmolkit.CleanupError property) Valence (cosmolkit.CleanupErrorKind attribute) valence (cosmolkit.ConjugationError property) Valence (cosmolkit.ConjugationErrorKind attribute) (cosmolkit.DescriptorErrorKind attribute) (cosmolkit.DrawingErrorKind attribute) valence (cosmolkit.EnumerationError property) Valence (cosmolkit.EnumerationErrorKind attribute) (cosmolkit.FragmentWriteInputErrorKind attribute) valence (cosmolkit.GenerationError property) Valence (cosmolkit.GenerationErrorKind attribute) (cosmolkit.GraphBoundsErrorKind attribute) valence (cosmolkit.HybridizationError property) Valence (cosmolkit.HybridizationErrorKind attribute) valence (cosmolkit.HydrogenError property) Valence (cosmolkit.HydrogenErrorKind attribute) valence (cosmolkit.KekulizeError property) Valence (cosmolkit.KekulizeErrorKind attribute) valence (cosmolkit.LegacyStereoError property) Valence (cosmolkit.LegacyStereoErrorKind attribute) (cosmolkit.MaccsFingerprintErrorKind attribute) valence (cosmolkit.MmffBuilderError property) Valence (cosmolkit.MmffBuilderErrorKind attribute) valence (cosmolkit.MmffMolPropertiesError property) Valence (cosmolkit.MmffMolPropertiesErrorKind attribute) (cosmolkit.MolProcessingErrorKind attribute) valence (cosmolkit.MolWriteError property) Valence (cosmolkit.MolWriteErrorKind attribute) (cosmolkit.MorganErrorKind attribute) valence (cosmolkit.OperationError property) Valence (cosmolkit.OperationErrorKind attribute) (cosmolkit.PdbPostprocessErrorKind attribute) (cosmolkit.PotentialStereoErrorKind attribute) valence (cosmolkit.PropertyCacheError property) Valence (cosmolkit.PropertyCacheErrorKind attribute) valence (cosmolkit.QueryMatchContextError property) Valence (cosmolkit.QueryMatchContextErrorKind attribute) valence (cosmolkit.RadicalError property) Valence (cosmolkit.RadicalErrorKind attribute) valence (cosmolkit.ReactionProductError property) Valence (cosmolkit.ReactionProductErrorKind attribute) valence (cosmolkit.ScaffoldError property) Valence (cosmolkit.ScaffoldErrorKind attribute) (cosmolkit.SmartsTraversalErrorKind attribute) (cosmolkit.SmartsWriteErrorKind attribute) valence (cosmolkit.SmilesStereoError property) Valence (cosmolkit.SmilesStereoErrorKind attribute) (cosmolkit.StereoReadErrorKind attribute) valence (cosmolkit.TautomerRunError property) Valence (cosmolkit.TautomerRunErrorKind attribute) (cosmolkit.UffBuilderErrorKind attribute) ValenceAssignmentLength (cosmolkit.AdjustHsErrorKind attribute) (cosmolkit.AromaticityErrorKind attribute) (cosmolkit.ConjugationErrorKind attribute) (cosmolkit.HybridizationErrorKind attribute) (cosmolkit.HydrogenErrorKind attribute) ValenceAssignmentLengthMismatch (cosmolkit.FragmentWriteInputErrorKind attribute) (cosmolkit.UffBuilderErrorKind attribute) ValenceError ValenceErrorKind (class in cosmolkit) ValenceModel (class in cosmolkit) ValenceOutOfRange (cosmolkit.SearchMcsErrorKind attribute) ValenceParams (class in cosmolkit) ValencePhase (class in cosmolkit) ValencePrecondition (cosmolkit.QueryMatchContextErrorKind attribute) ValenceRowCount (cosmolkit.CipRankErrorKind attribute) (cosmolkit.ScaffoldErrorKind attribute) ValenceRows (cosmolkit.QueryMatchContextErrorKind attribute) (cosmolkit.SmilesStereoErrorKind attribute) valences (cosmolkit.ElementInfo attribute) valid_count (cosmolkit.MoleculeBatch attribute) valid_mask (cosmolkit.MoleculeBatch attribute) valid_up_to (cosmolkit.AtomPropertyReadError property) (cosmolkit.MmjsonValueError property) (cosmolkit.PdbCrystalError attribute) (cosmolkit.PdbHeaderError property) (cosmolkit.PdbLinkRecordError attribute) (cosmolkit.PdbModResError attribute) (cosmolkit.PdbMtrixError attribute) (cosmolkit.PdbRemark200Error attribute) (cosmolkit.PdbRemark350Error attribute) (cosmolkit.PdbRemark3Error attribute) (cosmolkit.PdbRemarkError property) (cosmolkit.PdbSheetError attribute) (cosmolkit.PdbStructureFinalizationError attribute) (cosmolkit.Utf8Error property) validate() (cosmolkit.BioStructure method) (cosmolkit.Reaction method) validate_batch_params() (cosmolkit.SdfRecordStream static method) validate_for_atom_count() (cosmolkit.TemplateAttachmentOrder method) validate_parts() (cosmolkit.BioStructure static method) validate_with_params() (cosmolkit.Reaction method) Validation (cosmolkit.ReactionInitializationErrorKind attribute) value (cosmolkit.AdjustHsError property) (cosmolkit.AltLocLabel attribute) (cosmolkit.AromaticityError property) (cosmolkit.AtomQueryPredicate attribute) (cosmolkit.AtomRangeBounds attribute) (cosmolkit.BioMoleculeConversionError property) (cosmolkit.BioPdbWriteError property) (cosmolkit.BioStructureError property) (cosmolkit.BondQueryPredicate attribute) (cosmolkit.CanonicalRankError property) (cosmolkit.ChemCompAtomError property) (cosmolkit.ChemCompModelError property) (cosmolkit.CipDescriptorError property) (cosmolkit.CipRankError property) (cosmolkit.ConjugationError property) (cosmolkit.CoordinateInputError property) (cosmolkit.DoubleBondStereoError property) (cosmolkit.EmbedSeedError property) (cosmolkit.FingerprintError property) (cosmolkit.HybridizationError property) Value (cosmolkit.LayeredFingerprintErrorKind attribute) (cosmolkit.MaccsFingerprintErrorKind attribute) value (cosmolkit.McsError property) (cosmolkit.MmcifAtomSiteGroupingError property) (cosmolkit.MmcifAtomSiteScalarError property) (cosmolkit.MmcifCisPepError property) (cosmolkit.MmcifConnectionError property) (cosmolkit.MmcifHelixError property) (cosmolkit.MmcifLabelAddressError property) (cosmolkit.MmcifModResError property) (cosmolkit.MmcifSheetError property) (cosmolkit.MmcifSiftsUnpError property) (cosmolkit.MmjsonValueError property) (cosmolkit.MolPostError property) (cosmolkit.MolWriteError property) Value (cosmolkit.MolWriteErrorKind attribute) (cosmolkit.PatternFingerprintErrorKind attribute) value (cosmolkit.PdbPostprocessError property) (cosmolkit.PickleError property) (cosmolkit.PotentialStereoError property) (cosmolkit.PropertyIntReadError property) (cosmolkit.PropertyUIntReadError property) (cosmolkit.PropertyULongReadError property) (cosmolkit.ReactionValidationError property) Value (cosmolkit.RingFindingErrorKind attribute) value (cosmolkit.SdfGraph.Molecule attribute) (cosmolkit.SdfGraph.Query attribute) (cosmolkit.SdfReadError property) (cosmolkit.SdfWriteError property) (cosmolkit.SmartsWriteError property) (cosmolkit.StereoError property) Value (cosmolkit.TopologicalFingerprintErrorKind attribute) value (cosmolkit.TransformError property) (cosmolkit.UffBuilderError property) (cosmolkit.UffParamError property) (cosmolkit.ValenceError property) (cosmolkit.WedgeError property) (cosmolkit.XyzReadError property) value() (cosmolkit.BioAtom method) (cosmolkit.BioChain method) (cosmolkit.BioModel method) (cosmolkit.BioResidue method) (cosmolkit.MoleculeAtom method) (cosmolkit.SparseCountFingerprint method) (cosmolkit.SparseCountFingerprint32 method) value_bits (cosmolkit.DoubleLexicalReadError property) ValueCount (cosmolkit.AttachmentExpansionErrorKind attribute) values (cosmolkit.AdjacencyErrorKind attribute) (cosmolkit.AdjustHsErrorKind attribute) (cosmolkit.AlignmentErrorKind attribute) (cosmolkit.AromaticityErrorKind attribute) (cosmolkit.AromaticityModel attribute) (cosmolkit.AtomCodeErrorKind attribute) (cosmolkit.AtomCodeExplanationErrorKind attribute) (cosmolkit.AtomPairErrorKind attribute) (cosmolkit.AtomPairReadErrorKind attribute) (cosmolkit.AtomPathSubsetCopyErrorKind attribute) (cosmolkit.AtomPropertyErrorKind attribute) (cosmolkit.AtomPropertyReadErrorKind attribute) (cosmolkit.AtomQueryPredicateKind attribute) (cosmolkit.AtomRangeBoundsKind attribute) (cosmolkit.AtomRangeDataFunctionKind attribute) (cosmolkit.AtomSiteIdentityField attribute) (cosmolkit.AtropisomerErrorKind attribute) (cosmolkit.AttachmentExpansionErrorKind attribute) (cosmolkit.AutomaticForceFieldConstructionErrorKind attribute) (cosmolkit.AvalonEngineErrorKind attribute) (cosmolkit.AvalonFingerprintErrorKind attribute) (cosmolkit.BatchErrorMode attribute) (cosmolkit.BatchFingerprintOutputErrorKind attribute) (cosmolkit.BatchImageErrorKind attribute) (cosmolkit.BioAssemblySpecialKind attribute) (cosmolkit.BioAsu attribute) (cosmolkit.BioCalcFlag attribute) (cosmolkit.BioConnectionKind attribute) (cosmolkit.BioCoordinateFormat attribute) (cosmolkit.BioHelixClass attribute) (cosmolkit.BioMmcifReadStage attribute) (cosmolkit.BioMmcifWriteErrorKind attribute) (cosmolkit.BioMoleculeConversionErrorKind attribute) (cosmolkit.BioMoleculeErrorKind attribute) (cosmolkit.BioOperationErrorKind attribute) (cosmolkit.BioPdbReadStage attribute) (cosmolkit.BioPdbWriteErrorKind attribute) (cosmolkit.BioReadErrorKind attribute) (cosmolkit.BioRowChainErrorKind attribute) (cosmolkit.BioRowModelErrorKind attribute) (cosmolkit.BioRowTraverseErrorKind attribute) (cosmolkit.BioSelectionCopyCauseKind attribute) (cosmolkit.BioSelectionParseErrorKind attribute) (cosmolkit.BioSoftwareClassification attribute) (cosmolkit.BioStructureErrorKind attribute) (cosmolkit.BondDirection attribute) (cosmolkit.BondDirectionStereoErrorKind attribute) (cosmolkit.BondEndPointsParseErrorKind attribute) (cosmolkit.BondOrder attribute) (cosmolkit.BondQueryPredicateKind attribute) (cosmolkit.BondStereo attribute) (cosmolkit.BondValueErrorKind attribute) (cosmolkit.BoundKind attribute) (cosmolkit.BoundsMatrixErrorKind attribute) (cosmolkit.BoundsQueryErrorKind attribute) (cosmolkit.CanonicalRankErrorKind attribute) (cosmolkit.ChainKind attribute) (cosmolkit.ChemCompAtomErrorKind attribute) (cosmolkit.ChemCompModelErrorKind attribute) (cosmolkit.ChemistryProblemErrorKind attribute) (cosmolkit.ChiralTag attribute) (cosmolkit.CifReadErrorKind attribute) (cosmolkit.CipDescriptor attribute) (cosmolkit.CipDescriptorErrorKind attribute) (cosmolkit.CipLabelerErrorKind attribute) (cosmolkit.CipRankErrorKind attribute) (cosmolkit.CleanupErrorKind attribute) (cosmolkit.ConformerErrorKind attribute) (cosmolkit.ConformerOptimizerCauseKind attribute) (cosmolkit.ConjugationErrorKind attribute) (cosmolkit.Coordinate2DErrorKind attribute) (cosmolkit.Coordinate2DLayoutErrorKind attribute) (cosmolkit.Coordinate2DTemplateErrorKind attribute) (cosmolkit.Coordinate3DReadErrorKind attribute) (cosmolkit.CoordinateBlockSelectionErrorKind attribute) (cosmolkit.CoordinateDimension attribute) (cosmolkit.CoordinateInputErrorKind attribute) (cosmolkit.CoordinateValidationErrorKind attribute) (cosmolkit.CoordinateZPolicy attribute) (cosmolkit.CrystalffTorsionPreferencesErrorKind attribute) (cosmolkit.CxQueryLoweringErrorKind attribute) (cosmolkit.CxStereoGroupMergeErrorKind attribute) (cosmolkit.DenseMatrix attribute) (cosmolkit.DescriptorErrorKind attribute) (cosmolkit.DescriptorReadErrorKind attribute) (cosmolkit.DescriptorSearchCauseKind attribute) (cosmolkit.DispatchedUffOptimizationErrorKind attribute) (cosmolkit.DistGeomForceFieldErrorKind attribute) (cosmolkit.DoubleBondStereoErrorKind attribute) (cosmolkit.DoubleLexicalReadErrorKind attribute) (cosmolkit.DrawingErrorKind attribute) (cosmolkit.DrawingWriteErrorKind attribute) (cosmolkit.EmbedFailureCause attribute) (cosmolkit.EmbedFailureCountErrorKind attribute) (cosmolkit.EmbedSeedErrorKind attribute) (cosmolkit.EmbedTermination attribute) (cosmolkit.EntityKind attribute) (cosmolkit.EnumerationErrorKind attribute) (cosmolkit.FingerprintBatchErrorKind attribute) (cosmolkit.FingerprintErrorKind attribute) (cosmolkit.FingerprintJsonErrorKind attribute) (cosmolkit.FingerprintPreparationErrorKind attribute) (cosmolkit.FingerprintWorkerErrorKind attribute) (cosmolkit.ForceFieldAngleIndexArgument attribute) (cosmolkit.ForceFieldAngleRangeBound attribute) (cosmolkit.ForceFieldBondIndexArgument attribute) (cosmolkit.ForceFieldConstructionErrorKind attribute) (cosmolkit.ForceFieldIndexArgument attribute) (cosmolkit.ForceFieldKernelErrorKind attribute) (cosmolkit.ForceFieldTorsionIndexArgument attribute) (cosmolkit.FragmentCoordinateViewErrorKind attribute) (cosmolkit.FragmentWriteInputErrorKind attribute) (cosmolkit.FullCopyComponentErrorKind attribute) (cosmolkit.GenerationErrorKind attribute) (cosmolkit.GenerationFailureKind attribute) (cosmolkit.GraphBoundsErrorKind attribute) (cosmolkit.Hybridization attribute) (cosmolkit.HybridizationErrorKind attribute) (cosmolkit.HydrogenErrorKind attribute) (cosmolkit.InchiDiagnosticLevel attribute) (cosmolkit.InchiErrorKind attribute) (cosmolkit.JsonErrorKind attribute) (cosmolkit.KekulizeErrorKind attribute) (cosmolkit.LayeredFingerprintErrorKind attribute) (cosmolkit.LegacyStereoErrorKind attribute) (cosmolkit.MaccsFingerprintErrorKind attribute) (cosmolkit.MappingValidationErrorKind attribute) (cosmolkit.MatchErrorKind attribute) (cosmolkit.MatrixAxis attribute) (cosmolkit.MatrixErrorKind attribute) (cosmolkit.McsAtomComparator attribute) (cosmolkit.McsBondComparator attribute) (cosmolkit.McsErrorKind attribute) (cosmolkit.McsProgressErrorKind attribute) (cosmolkit.MmcifAssemblyErrorKind attribute) (cosmolkit.MmcifAtomSiteGroupingErrorKind attribute) (cosmolkit.MmcifAtomSiteScalarErrorKind attribute) (cosmolkit.MmcifCcdRestoreErrorKind attribute) (cosmolkit.MmcifCisPepErrorKind attribute) (cosmolkit.MmcifConnectionErrorKind attribute) (cosmolkit.MmcifCrystalInfoErrorKind attribute) (cosmolkit.MmcifEntityInfoErrorKind attribute) (cosmolkit.MmcifHelixErrorKind attribute) (cosmolkit.MmcifLabelAddressErrorKind attribute) (cosmolkit.MmcifModResErrorKind attribute) (cosmolkit.MmcifOperationExprErrorKind attribute) (cosmolkit.MmcifSequenceIdErrorKind attribute) (cosmolkit.MmcifSheetErrorKind attribute) (cosmolkit.MmcifSiftsUnpErrorKind attribute) (cosmolkit.MmcifTlsInfoErrorKind attribute) (cosmolkit.MmffAngleLookupErrorKind attribute) (cosmolkit.MmffBuilderErrorKind attribute) (cosmolkit.MmffMolPropertiesErrorKind attribute) (cosmolkit.MmffOopLookupErrorKind attribute) (cosmolkit.MmffOptimizationFailureKind attribute) (cosmolkit.MmffParamErrorKind attribute) (cosmolkit.MmffParamParseCauseKind attribute) (cosmolkit.MmffParamTable attribute) (cosmolkit.MmffTorLookupErrorKind attribute) (cosmolkit.MmffVariant attribute) (cosmolkit.MmffVdwParseErrorKind attribute) (cosmolkit.MmjsonReadErrorKind attribute) (cosmolkit.MmjsonStructureErrorKind attribute) (cosmolkit.MmjsonUnexpectedType attribute) (cosmolkit.MmjsonValueErrorKind attribute) (cosmolkit.Mol2ReadErrorKind attribute) (cosmolkit.Mol2Type attribute) (cosmolkit.MolecularForceFieldErrorKind attribute) (cosmolkit.MolecularIoErrorKind attribute) (cosmolkit.MoleculeFragmentsFailureKind attribute) (cosmolkit.MoleculeHashErrorKind attribute) (cosmolkit.MoleculeOpOutput attribute) (cosmolkit.MoleculePropertyErrorKind attribute) (cosmolkit.MoleculeTransferErrorKind attribute) (cosmolkit.MolPostErrorKind attribute) (cosmolkit.MolProcessingErrorKind attribute) (cosmolkit.MolWriteErrorKind attribute) (cosmolkit.MorganErrorKind attribute) (cosmolkit.MorganReadErrorKind attribute) (cosmolkit.NonbondedAssemblyErrorKind attribute) (cosmolkit.NonbondedFragmentMappingErrorKind attribute) (cosmolkit.OperationError property) (cosmolkit.OperationErrorKind attribute) (cosmolkit.OptimizationStageErrorKind attribute) (cosmolkit.OptimizationStatus attribute) (cosmolkit.OrderedFragmentBuildErrorKind attribute) (cosmolkit.ParityPolicy attribute) (cosmolkit.ParserCarrierErrorKind attribute) (cosmolkit.ParserStereoOrderErrorKind attribute) (cosmolkit.PathErrorKind attribute) (cosmolkit.PatternFingerprintErrorKind attribute) (cosmolkit.PdbAtomFieldErrorKind attribute) (cosmolkit.PdbCisPepRecordErrorKind attribute) (cosmolkit.PdbConectErrorKind attribute) (cosmolkit.PdbConnectionFinalizationErrorKind attribute) (cosmolkit.PdbCrystalErrorKind attribute) (cosmolkit.PdbDbRefErrorKind attribute) (cosmolkit.PdbHeaderErrorKind attribute) (cosmolkit.PdbHelixErrorKind attribute) (cosmolkit.PdbInputFormatErrorKind attribute) (cosmolkit.PdbLinkNameCounter attribute) (cosmolkit.PdbLinkRecordErrorKind attribute) (cosmolkit.PdbModelTransitionErrorKind attribute) (cosmolkit.PdbModResErrorKind attribute) (cosmolkit.PdbMtrixErrorKind attribute) (cosmolkit.PdbPostprocessErrorKind attribute) (cosmolkit.PdbReaderCauseKind attribute) (cosmolkit.PdbRemark200ErrorKind attribute) (cosmolkit.PdbRemark350ErrorKind attribute) (cosmolkit.PdbRemark3ErrorKind attribute) (cosmolkit.PdbRemarkErrorKind attribute) (cosmolkit.PdbRemarkFinalizationErrorKind attribute) (cosmolkit.PdbRemarkMetadataErrorKind attribute) (cosmolkit.PdbResidueKeyErrorKind attribute) (cosmolkit.PdbSheetErrorKind attribute) (cosmolkit.PdbSsbondRecordErrorKind attribute) (cosmolkit.PdbStructureFinalizationErrorKind attribute) (cosmolkit.PdbWriteErrorKind attribute) (cosmolkit.PeriodicTableErrorKind attribute) (cosmolkit.PickleErrorKind attribute) (cosmolkit.PolymerKind attribute) (cosmolkit.PotentialStereoDescriptor attribute) (cosmolkit.PotentialStereoErrorKind attribute) (cosmolkit.PotentialStereoSpecified attribute) (cosmolkit.PotentialStereoType attribute) (cosmolkit.PropertyCacheErrorKind attribute) (cosmolkit.PropertyIntReadErrorKind attribute) (cosmolkit.PropertyStringErrorKind attribute) (cosmolkit.PropertyUIntReadErrorKind attribute) (cosmolkit.PropertyULongReadErrorKind attribute) (cosmolkit.PropertyValueKind attribute) (cosmolkit.ProteinProjectionErrorKind attribute) (cosmolkit.ProteinReadErrorKind attribute) (cosmolkit.PruningErrorKind attribute) (cosmolkit.QueryAtomConversionErrorKind attribute) (cosmolkit.QueryCompileErrorKind attribute) (cosmolkit.QueryGraphErrorKind attribute) (cosmolkit.QueryMatchContextErrorKind attribute) (cosmolkit.QueryStateErrorKind attribute) (cosmolkit.RadicalErrorKind attribute) (cosmolkit.ReactionApplyErrorKind attribute) (cosmolkit.ReactionInitializationErrorKind attribute) (cosmolkit.ReactionModelErrorKind attribute) (cosmolkit.ReactionParseErrorKind attribute) (cosmolkit.ReactionProductErrorKind attribute) (cosmolkit.ReactionRole attribute) (cosmolkit.ReactionRunErrorKind attribute) (cosmolkit.ReactionValidationErrorKind attribute) (cosmolkit.ReactionValidationIssueKind attribute) (cosmolkit.ReactionValidationSeverity attribute) (cosmolkit.ReactionWriteErrorKind attribute) (cosmolkit.RequiredPropertyStringErrorKind attribute) (cosmolkit.ResidueCode attribute) (cosmolkit.ResidueInfoKind attribute) (cosmolkit.ResidueKind attribute) (cosmolkit.ResidueSequenceErrorKind attribute) (cosmolkit.RingDecomposerErrorKind attribute) (cosmolkit.RingFindingErrorKind attribute) (cosmolkit.RotatableBondsOptions attribute) (cosmolkit.SanitizeErrorKind attribute) (cosmolkit.SanitizeStage attribute) (cosmolkit.ScaffoldErrorKind attribute) (cosmolkit.SdfCoordinateMode attribute) (cosmolkit.SdfErrorKind attribute) (cosmolkit.SdfFormat attribute) (cosmolkit.SdfPropertyList attribute) (cosmolkit.SdfPropertyListTarget attribute) (cosmolkit.SdfReadErrorKind attribute) (cosmolkit.SdfWriteErrorKind attribute) (cosmolkit.SearchMcsErrorKind attribute) (cosmolkit.SelectedBondCopyErrorKind attribute) (cosmolkit.SelectedSubstanceGroupCopyErrorKind attribute) (cosmolkit.SerdeJsonCategory attribute) (cosmolkit.SerialConformerOptimizationErrorKind attribute) (cosmolkit.SerialUffOptimizationErrorKind attribute) (cosmolkit.SingleConformerOptimizationErrorKind attribute) (cosmolkit.SmartsParseErrorKind attribute) (cosmolkit.SmartsTraversalErrorKind attribute) (cosmolkit.SmartsWriteErrorKind attribute) (cosmolkit.SmilesErrorKind attribute) (cosmolkit.SmilesParseErrorKind attribute) (cosmolkit.SmilesStereoErrorKind attribute) (cosmolkit.SmilesWriteErrorKind attribute) (cosmolkit.StereoErrorKind attribute) (cosmolkit.StereoGroupErrorKind attribute) (cosmolkit.StereoGroupKind attribute) (cosmolkit.StereoOrderErrorKind attribute) (cosmolkit.StereoReadErrorKind attribute) (cosmolkit.SubstanceGroupAtomList attribute) (cosmolkit.SubstructMatchErrorKind attribute) (cosmolkit.SvgParseErrorKind attribute) (cosmolkit.TautomerCatalogErrorKind attribute) (cosmolkit.TautomerEnumerationStatus attribute) (cosmolkit.TautomerRunErrorKind attribute) (cosmolkit.TautomerTransformErrorKind attribute) (cosmolkit.TemplateAttachmentOrderErrorKind attribute) (cosmolkit.ThreadCountErrorKind attribute) (cosmolkit.TopologicalFingerprintErrorKind attribute) (cosmolkit.TopologicalTorsionErrorKind attribute) (cosmolkit.TopologicalTorsionPathScoreErrorKind attribute) (cosmolkit.TopologicalTorsionReadErrorKind attribute) (cosmolkit.TopologyEditErrorKind attribute) (cosmolkit.TopologyValidationErrorKind attribute) (cosmolkit.TransformErrorKind attribute) (cosmolkit.UffBondMathErrorKind attribute) (cosmolkit.UffBoundsCauseKind attribute) (cosmolkit.UffBuilderErrorKind attribute) (cosmolkit.UffDefaultTorsionQueryErrorKind attribute) (cosmolkit.UffEvaluationFailureKind attribute) (cosmolkit.UffInversionContributionErrorKind attribute) (cosmolkit.UffInversionIndexArgument attribute) (cosmolkit.UffParamErrorKind attribute) (cosmolkit.UffParameterErrorKind attribute) (cosmolkit.UffParameterQueryErrorKind attribute) (cosmolkit.UffPreparedOptimizationErrorKind attribute) (cosmolkit.UffPreparedValenceField attribute) (cosmolkit.UffThreadCountErrorKind attribute) (cosmolkit.UffTorsionBondQueryErrorKind attribute) (cosmolkit.UffTypingErrorKind attribute) (cosmolkit.UffTypingInput attribute) (cosmolkit.UIntLexicalReadErrorKind attribute) (cosmolkit.UnsignedStreamArrayErrorKind attribute) (cosmolkit.ValenceErrorKind attribute) (cosmolkit.ValenceModel attribute) (cosmolkit.ValencePhase attribute) (cosmolkit.WedgeErrorKind attribute) (cosmolkit.XmlParseErrorKind attribute) (cosmolkit.XyzReadErrorKind attribute) (cosmolkit.XyzWriteErrorKind attribute) variant (cosmolkit.AdjacencyError property) (cosmolkit.AdjustHsError property) (cosmolkit.AlignmentError property) (cosmolkit.AromaticityError property) (cosmolkit.AtomCodeError property) (cosmolkit.AtomCodeExplanationError property) (cosmolkit.AtomPairError property) (cosmolkit.AtomPairReadError property) (cosmolkit.AtomPathSubsetCopyError property) (cosmolkit.AtomPropertyError property) (cosmolkit.AtomPropertyReadError property) (cosmolkit.AtomQueryPredicate attribute) (cosmolkit.AtomRangeBounds attribute) (cosmolkit.AtomRangeDataFunction attribute) (cosmolkit.AtropisomerError property) (cosmolkit.AttachmentExpansionError property) (cosmolkit.AutomaticForceFieldConstructionError property) (cosmolkit.AvalonEngineError property) (cosmolkit.AvalonFingerprintError property) (cosmolkit.BatchFingerprintOutputError property) (cosmolkit.BatchImageError property) (cosmolkit.BioMmcifWriteError property) (cosmolkit.BioMoleculeConversionError property) (cosmolkit.BioMoleculeError property) (cosmolkit.BioOperationError property) (cosmolkit.BioPdbWriteError property) (cosmolkit.BioReadError property) (cosmolkit.BioRowChainError property) (cosmolkit.BioRowModelError property) (cosmolkit.BioRowTraverseError property) (cosmolkit.BioSelectionCopyCause property) (cosmolkit.BioSelectionParseError property) (cosmolkit.BioStructureError property) (cosmolkit.BondDirectionStereoError property) (cosmolkit.BondQueryPredicate attribute) (cosmolkit.BondValueError property) (cosmolkit.BoundsMatrixError property) (cosmolkit.BoundsQueryError property) (cosmolkit.CanonicalRankError property) (cosmolkit.ChemCompAtomError property) (cosmolkit.ChemCompModelError property) (cosmolkit.ChemistryProblemError property) (cosmolkit.CipDescriptorError property) (cosmolkit.CipLabelerError property) (cosmolkit.CipRankError property) (cosmolkit.CleanupError property) (cosmolkit.ConformerError property) (cosmolkit.ConformerOptimizerCause attribute) (cosmolkit.ConjugationError property) (cosmolkit.Coordinate2DError property) (cosmolkit.Coordinate2DLayoutError property) (cosmolkit.Coordinate2DTemplateError property) (cosmolkit.Coordinate3DReadError property) (cosmolkit.CoordinateBlockSelectionError property) (cosmolkit.CoordinateInputError property) (cosmolkit.CoordinateValidationError property) (cosmolkit.CrystalffTorsionPreferencesError property) (cosmolkit.CxQueryLoweringError property) (cosmolkit.CxStereoGroupMergeError property) (cosmolkit.DescriptorError property) (cosmolkit.DescriptorReadError property) (cosmolkit.DescriptorSearchCause property) (cosmolkit.DispatchedUffOptimizationError property) (cosmolkit.DistGeomForceFieldError attribute) (cosmolkit.DoubleBondStereoError property) (cosmolkit.DrawingError property) (cosmolkit.DrawingWriteError property) (cosmolkit.EmbedFailureCountError property) (cosmolkit.EmbedSeedError property) (cosmolkit.EnumerationError property) (cosmolkit.FingerprintBatchError property) (cosmolkit.FingerprintError property) (cosmolkit.FingerprintJsonError property) (cosmolkit.FingerprintPreparationError property) (cosmolkit.FingerprintWorkerError property) (cosmolkit.ForceFieldConstructionError property) (cosmolkit.ForceFieldKernelError property) (cosmolkit.FragmentCoordinateViewError property) (cosmolkit.FragmentWriteInputError property) (cosmolkit.FullCopyComponentError property) (cosmolkit.GenerationError property) (cosmolkit.GenerationFailure property) (cosmolkit.GraphBoundsError property) (cosmolkit.HybridizationError property) (cosmolkit.HydrogenError property) (cosmolkit.InchiError property) (cosmolkit.KekulizeError property) (cosmolkit.LayeredFingerprintError property) (cosmolkit.LegacyStereoError property) (cosmolkit.MaccsFingerprintError property) (cosmolkit.MappingValidationError property) (cosmolkit.MatchError property) (cosmolkit.MatrixError property) (cosmolkit.McsError property) (cosmolkit.McsProgressError property) (cosmolkit.MmcifAssemblyError property) (cosmolkit.MmcifAtomSiteGroupingError property) (cosmolkit.MmcifAtomSiteScalarError property) (cosmolkit.MmcifCcdRestoreError property) (cosmolkit.MmcifCisPepError property) (cosmolkit.MmcifConnectionError property) (cosmolkit.MmcifCrystalInfoError property) (cosmolkit.MmcifEntityInfoError property) (cosmolkit.MmcifHelixError property) (cosmolkit.MmcifLabelAddressError property) (cosmolkit.MmcifModResError property) (cosmolkit.MmcifOperationExprError property) (cosmolkit.MmcifSequenceIdError property) (cosmolkit.MmcifSheetError property) (cosmolkit.MmcifSiftsUnpError property) (cosmolkit.MmcifTlsInfoError property) (cosmolkit.MmffAngleLookupError property) (cosmolkit.MmffBuilderError property) (cosmolkit.MmffMolPropertiesError property) (cosmolkit.MmffOopLookupError property) (cosmolkit.MmffOptimizationFailure property) (cosmolkit.MmffParamError property) (cosmolkit.MmffParamParseCause attribute) (cosmolkit.MmffProperties attribute) (cosmolkit.MmffTorLookupError property) (cosmolkit.MmffVdwParseError property) (cosmolkit.MmjsonReadError property) (cosmolkit.MmjsonStructureError property) (cosmolkit.MmjsonValueError property) (cosmolkit.Mol2ReadError property) (cosmolkit.Mol2ReadParams attribute) (cosmolkit.MolecularIoError property) (cosmolkit.MoleculeFragmentsFailure property) (cosmolkit.MoleculeHashError property) (cosmolkit.MoleculePropertyError property) (cosmolkit.MoleculeTransferError property) (cosmolkit.MolPostError property) (cosmolkit.MolProcessingError property) (cosmolkit.MolWriteError property) (cosmolkit.MorganError property) (cosmolkit.MorganReadError property) (cosmolkit.NonbondedAssemblyError property) (cosmolkit.NonbondedFragmentMappingError property) (cosmolkit.OperationError property) (cosmolkit.OptimizationStageError property) (cosmolkit.OrderedFragmentBuildError property) (cosmolkit.ParserCarrierError property) (cosmolkit.ParserStereoOrderError property) (cosmolkit.PathError property) (cosmolkit.PatternFingerprintError property) (cosmolkit.PdbAtomFieldError attribute) (cosmolkit.PdbCisPepRecordError attribute) (cosmolkit.PdbConectError attribute) (cosmolkit.PdbConnectionFinalizationError attribute) (cosmolkit.PdbCrystalError attribute) (cosmolkit.PdbDbRefError attribute) (cosmolkit.PdbHeaderError property) (cosmolkit.PdbHelixError attribute) (cosmolkit.PdbInputFormatError property) (cosmolkit.PdbLinkRecordError attribute) (cosmolkit.PdbModelTransitionError property) (cosmolkit.PdbModResError attribute) (cosmolkit.PdbMtrixError attribute) (cosmolkit.PdbPostprocessError property) (cosmolkit.PdbReaderCause property) (cosmolkit.PdbRemark200Error attribute) (cosmolkit.PdbRemark350Error attribute) (cosmolkit.PdbRemark3Error attribute) (cosmolkit.PdbRemarkError property) (cosmolkit.PdbRemarkFinalizationError attribute) (cosmolkit.PdbRemarkMetadataError attribute) (cosmolkit.PdbResidueKeyError property) (cosmolkit.PdbSheetError attribute) (cosmolkit.PdbSsbondRecordError attribute) (cosmolkit.PdbStructureFinalizationError attribute) (cosmolkit.PdbWriteError property) (cosmolkit.PeriodicTableError property) (cosmolkit.PickleError property) (cosmolkit.PotentialStereoError property) (cosmolkit.PropertyCacheError property) (cosmolkit.PropertyIntReadError property) (cosmolkit.PropertyStringError property) (cosmolkit.PropertyUIntReadError property) (cosmolkit.PropertyULongReadError property) (cosmolkit.ProteinProjectionError property) (cosmolkit.ProteinReadError property) (cosmolkit.PruningError property) (cosmolkit.QueryAtomConversionError property) (cosmolkit.QueryCompileError property) (cosmolkit.QueryGraphError property) (cosmolkit.QueryMatchContextError property) (cosmolkit.QueryStateError property) (cosmolkit.RadicalError property) (cosmolkit.ReactionApplyError property) (cosmolkit.ReactionInitializationError property) (cosmolkit.ReactionModelError property) (cosmolkit.ReactionParseError property) (cosmolkit.ReactionProductError property) (cosmolkit.ReactionRunError property) (cosmolkit.ReactionValidationError property) (cosmolkit.ReactionWriteError property) (cosmolkit.RequiredPropertyStringError property) (cosmolkit.ResidueSequenceError property) (cosmolkit.RingDecomposerError property) (cosmolkit.RingFindingError property) (cosmolkit.SanitizeError property) (cosmolkit.ScaffoldError property) (cosmolkit.SdfError property) (cosmolkit.SdfReadError property) (cosmolkit.SdfWriteError property) (cosmolkit.SearchMcsError property) (cosmolkit.SelectedBondCopyError property) (cosmolkit.SelectedSubstanceGroupCopyError property) (cosmolkit.SerialConformerOptimizationError property) (cosmolkit.SerialUffOptimizationError property) (cosmolkit.SingleConformerOptimizationError property) (cosmolkit.SmartsParseError property) (cosmolkit.SmartsTraversalError property) (cosmolkit.SmartsWriteError property) (cosmolkit.SmilesError property) (cosmolkit.SmilesParseError property) (cosmolkit.SmilesStereoError property) (cosmolkit.SmilesWriteError property) (cosmolkit.StereoError property) (cosmolkit.StereoGroupError property) (cosmolkit.StereoOrderError property) (cosmolkit.StereoReadError property) (cosmolkit.SubstructMatchError property) (cosmolkit.SvgParseError property) (cosmolkit.TautomerCatalogError property) (cosmolkit.TautomerRunError property) (cosmolkit.TautomerTransformError property) (cosmolkit.TemplateAttachmentOrderError property) (cosmolkit.ThreadCountError property) (cosmolkit.TopologicalFingerprintError property) (cosmolkit.TopologicalTorsionError property) (cosmolkit.TopologicalTorsionPathScoreError property) (cosmolkit.TopologicalTorsionReadError property) (cosmolkit.TopologyEditError property) (cosmolkit.TopologyValidationError property) (cosmolkit.TransformError property) (cosmolkit.UffBondMathError property) (cosmolkit.UffBoundsCause attribute) (cosmolkit.UffBuilderError property) (cosmolkit.UffDefaultTorsionQueryError property) (cosmolkit.UffEvaluationFailure attribute) (cosmolkit.UffInversionContributionError property) (cosmolkit.UffParamError property) (cosmolkit.UffParameterQueryError property) (cosmolkit.UffPreparedOptimizationError property) (cosmolkit.UffThreadCountError property) (cosmolkit.UffTorsionBondQueryError property) (cosmolkit.UffTypingError property) (cosmolkit.UIntLexicalReadError property) (cosmolkit.UnsignedStreamArrayError property) (cosmolkit.ValenceError property) (cosmolkit.WedgeError property) (cosmolkit.XmlParseError property) (cosmolkit.XyzReadError property) (cosmolkit.XyzWriteError property) VariationArray (cosmolkit.DrawingErrorKind attribute) VariationIndex (cosmolkit.DrawingErrorKind attribute) vdw (cosmolkit.MmffParamError property) Vdw (cosmolkit.MmffParamErrorKind attribute) (cosmolkit.MmffParamTable attribute) vdw_threshold (cosmolkit.UffConformerOptimizationParams attribute) (cosmolkit.UffEvaluationParams attribute) (cosmolkit.UffForceFieldParams attribute) (cosmolkit.UffOptimizationParams attribute) vector (cosmolkit.SGroupCState attribute) verbose (cosmolkit.EmbedParams attribute) (cosmolkit.McsParameters attribute) version (cosmolkit.BioSoftwareItem attribute) (cosmolkit.CrystalffTorsionPreferencesError property) (cosmolkit.PickleError property) version() (cosmolkit.AtomPairsParameters static method) (in module cosmolkit) VersionMismatch (cosmolkit.MoleculeTransferErrorKind attribute) volume (cosmolkit.BioCrystalInfo attribute) W W (cosmolkit.Element attribute) Warning (cosmolkit.InchiDiagnosticLevel attribute) (cosmolkit.ReactionValidationSeverity attribute) warnings (cosmolkit.ReactionValidationReport attribute) Water (cosmolkit.EntityKind attribute) (cosmolkit.ResidueKind attribute) WaterOnly (cosmolkit.ChainKind attribute) wavelengths (cosmolkit.BioDiffractionInfo attribute) Wedge (cosmolkit.DrawingErrorKind attribute) wedge (cosmolkit.MolWriteError property) Wedge (cosmolkit.MolWriteErrorKind attribute) WedgeAtomMismatch (cosmolkit.CxQueryLoweringErrorKind attribute) WedgeError WedgeErrorKind (class in cosmolkit) weight (cosmolkit.BioRefinementRestraint attribute) (cosmolkit.ResidueInfo attribute) weight_len (cosmolkit.AlignmentError property) WeightCount (cosmolkit.TransformErrorKind attribute) WeightCountMismatch (cosmolkit.AlignmentErrorKind attribute) weights (cosmolkit.AlignmentParameters attribute) (cosmolkit.AllConformerRmsdParameters attribute) (cosmolkit.BestAlignmentParameters attribute) (cosmolkit.ConformerAlignmentParameters attribute) (cosmolkit.CoordinateRmsdParameters attribute) what (cosmolkit.AtomCodeError property) (cosmolkit.FingerprintError property) width (cosmolkit.BatchImageParams attribute) (cosmolkit.DrawingError property) (cosmolkit.PdbHelixError attribute) (cosmolkit.PdbModResError attribute) (cosmolkit.PdbRemark350Error attribute) (cosmolkit.PdbRemark3Error attribute) (cosmolkit.PdbResidueKeyError property) (cosmolkit.PdbSheetError attribute) WidthMismatch (cosmolkit.FingerprintBatchErrorKind attribute) with_2d_coordinate_block() (cosmolkit.Molecule method) with_2d_coordinate_block_with_params() (cosmolkit.Molecule method) with_2d_coordinates() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) with_2d_coordinates_with_params() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) with_3d_conformer() (cosmolkit.Molecule method) with_3d_conformer_result() (cosmolkit.Molecule method) with_3d_conformer_result_with_params() (cosmolkit.Molecule method) with_3d_conformer_with_params() (cosmolkit.Molecule method) with_3d_conformers() (cosmolkit.Molecule method) with_3d_conformers_result() (cosmolkit.Molecule method) with_3d_conformers_result_with_params() (cosmolkit.Molecule method) with_3d_conformers_with_params() (cosmolkit.Molecule method) with_3d_coordinates() (cosmolkit.Molecule method) with_3d_coordinates_with_params() (cosmolkit.Molecule method) with_added() (cosmolkit.SparseCountFingerprint method) (cosmolkit.SparseCountFingerprint32 method) with_added_3d_conformer() (cosmolkit.Molecule method) with_added_3d_conformer_with_params() (cosmolkit.Molecule method) with_added_scalar() (cosmolkit.SparseCountFingerprint method) (cosmolkit.SparseCountFingerprint32 method) with_agent_template() (cosmolkit.Reaction method) with_aligned_conformers() (cosmolkit.Molecule method) with_aligned_conformers_with_params() (cosmolkit.Molecule method) with_alignment_to() (cosmolkit.Molecule method) with_alignment_to_with_params() (cosmolkit.Molecule method) with_assigned_aromaticity() (cosmolkit.Molecule method) with_assigned_aromaticity_with_params() (cosmolkit.Molecule method) with_assigned_radicals() (cosmolkit.Molecule method) with_assigned_ring_families() (cosmolkit.Molecule method) with_assigned_ring_families_with_params() (cosmolkit.Molecule method) with_assigned_rings() (cosmolkit.Molecule method) with_assigned_valence() (cosmolkit.Molecule method) with_assigned_valence_with_params() (cosmolkit.Molecule method) with_atom_map() (cosmolkit.AtomSpec method) with_atom_pair_atom_code() (cosmolkit.Molecule method) with_atom_position() (cosmolkit.Molecule method) with_atom_position_with_params() (cosmolkit.Molecule method) with_atom_property_bool() (cosmolkit.Molecule method) with_atom_property_double() (cosmolkit.Molecule method) with_atom_property_int() (cosmolkit.Molecule method) with_atom_property_int_vector() (cosmolkit.Molecule method) with_atom_property_string() (cosmolkit.Molecule method) with_atom_property_string_vector() (cosmolkit.Molecule method) with_atom_property_uint() (cosmolkit.Molecule method) with_chiral_tags_from_structure() (cosmolkit.Molecule method) with_chiral_tags_from_structure_with_params() (cosmolkit.Molecule method) with_cip_labels() (cosmolkit.Molecule method) with_cip_labels_with_options() (cosmolkit.Molecule method) with_cleared_3d_conformers() (cosmolkit.Molecule method) with_divided_scalar() (cosmolkit.SparseCountFingerprint method) (cosmolkit.SparseCountFingerprint32 method) with_explicit_hydrogens() (cosmolkit.AtomSpec method) with_formal_charge() (cosmolkit.AtomSpec method) with_hydrogens() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) with_hydrogens_with_params() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) with_id() (cosmolkit.StereoGroup method) with_implicit_properties() (cosmolkit.Reaction method) with_initialized() (cosmolkit.Reaction method) with_initialized_with_params() (cosmolkit.Reaction method) with_isotope() (cosmolkit.AtomSpec method) with_json() (cosmolkit.AtomPairGeneratorParams method) (cosmolkit.EmbedParams method) (cosmolkit.MorganGeneratorParams method) (cosmolkit.TopologicalTorsionGeneratorParams method) with_kekulized_bonds() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) with_kekulized_bonds_with_params() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) with_match_params() (cosmolkit.Reaction method) with_max_tautomers() (cosmolkit.TautomerParams method) with_max_transforms() (cosmolkit.TautomerParams method) with_mmff_optimized() (cosmolkit.Molecule method) with_mmff_optimized_conformers() (cosmolkit.Molecule method) with_mmff_optimized_conformers_with_params() (cosmolkit.Molecule method) with_mmff_optimized_with_params() (cosmolkit.Molecule method) with_multiplied_scalar() (cosmolkit.SparseCountFingerprint method) (cosmolkit.SparseCountFingerprint32 method) with_name() (cosmolkit.MoleculeBuilder method) with_no_implicit() (cosmolkit.AtomSpec method) with_only_3d_conformer() (cosmolkit.Molecule method) with_only_3d_conformer_with_params() (cosmolkit.Molecule method) with_parallel_jobs() (cosmolkit.MoleculeBatch method) with_product_template() (cosmolkit.Reaction method) with_progress_bar() (cosmolkit.MoleculeBatch method) with_properties() (cosmolkit.MoleculeBuilder method) with_property() (cosmolkit.MoleculeBuilder method) with_reactant_template() (cosmolkit.Reaction method) with_reassign_stereo() (cosmolkit.TautomerParams method) with_remove_bond_stereo() (cosmolkit.TautomerParams method) with_remove_isotopic_hydrogens() (cosmolkit.TautomerParams method) with_remove_sp3_stereo() (cosmolkit.TautomerParams method) with_sdf_data_field() (cosmolkit.MoleculeBuilder method) with_selection() (cosmolkit.BioStructure method) (cosmolkit.Protein method) with_subtracted() (cosmolkit.SparseCountFingerprint method) (cosmolkit.SparseCountFingerprint32 method) with_subtracted_scalar() (cosmolkit.SparseCountFingerprint method) (cosmolkit.SparseCountFingerprint32 method) with_translated_coordinates() (cosmolkit.BioStructure method) (cosmolkit.Protein method) with_uff_optimized() (cosmolkit.Molecule method) with_uff_optimized_conformers() (cosmolkit.Molecule method) with_uff_optimized_conformers_with_params() (cosmolkit.Molecule method) with_uff_optimized_with_params() (cosmolkit.Molecule method) with_valid_records() (cosmolkit.MoleculeBatch method) with_write_id() (cosmolkit.StereoGroup method) without_agents() (cosmolkit.Reaction method) without_hydrogens() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) without_hydrogens_with_params() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) without_unmapped_products() (cosmolkit.Reaction method) without_unmapped_products_with_params() (cosmolkit.Reaction method) without_unmapped_reactants() (cosmolkit.Reaction method) without_unmapped_reactants_with_params() (cosmolkit.Reaction method) work_set_count (cosmolkit.BioBasicRefinementInfo attribute) Worker (cosmolkit.MorganErrorKind attribute) WorkerLaunch (cosmolkit.GenerationErrorKind attribute) WorkerPanic (cosmolkit.TopologicalTorsionErrorKind attribute) WorkerProtocol (cosmolkit.TopologicalTorsionErrorKind attribute) WorkerTerminated (cosmolkit.AlignmentErrorKind attribute) WouldBlock (cosmolkit.IoErrorKind attribute) Write (cosmolkit.BatchImageErrorKind attribute) (cosmolkit.SmilesWriteErrorKind attribute) write_cx_smarts() (in module cosmolkit) write_id (cosmolkit.StereoGroup attribute) write_images() (cosmolkit.MoleculeBatch method) write_images_with_params() (cosmolkit.MoleculeBatch method) write_mmcif() (cosmolkit.BioStructure method) write_mmcif_with_params() (cosmolkit.BioStructure method) write_mol() (cosmolkit.Molecule method) write_mol_with_params() (cosmolkit.Molecule method) write_pdb() (cosmolkit.BioStructure method) write_pdb_with_params() (cosmolkit.BioStructure method) write_png() (cosmolkit.Molecule method) write_report() (cosmolkit.BatchExportReport method) write_sdf() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) write_sdf_files() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) write_sdf_files_with_params() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) write_sdf_with_params() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) write_smarts() (in module cosmolkit) write_svg() (cosmolkit.Molecule method) write_xyz() (cosmolkit.Molecule method) write_xyz_with_params() (cosmolkit.Molecule method) Writer (cosmolkit.FragmentWriteInputErrorKind attribute) writer_canonical_invariant (cosmolkit.SmilesParseError property) writer_stereo (cosmolkit.SmilesParseError property) writer_valence (cosmolkit.SmilesParseError property) WriterCanonicalInvariant (cosmolkit.SmilesParseErrorKind attribute) WriterInt (cosmolkit.SmilesParseErrorKind attribute) WriterKekulize (cosmolkit.SmilesParseErrorKind attribute) WriterLegacyStereo (cosmolkit.SmilesParseErrorKind attribute) WriterNumeric (cosmolkit.SmilesParseErrorKind attribute) WriterParserStereoOrder (cosmolkit.SmilesParseErrorKind attribute) WriterPotentialStereo (cosmolkit.SmilesParseErrorKind attribute) WriterProperty (cosmolkit.SmilesParseErrorKind attribute) WriterPropertyKind (cosmolkit.SmilesParseErrorKind attribute) WriterPropertyList (cosmolkit.SmilesParseErrorKind attribute) WriterRequiredProperty (cosmolkit.SmilesParseErrorKind attribute) WriterRings (cosmolkit.SmilesParseErrorKind attribute) WriterRootAtomOutOfRange (cosmolkit.SmilesParseErrorKind attribute) WriterStereo (cosmolkit.SmilesParseErrorKind attribute) WriterStereoBond (cosmolkit.SmilesParseErrorKind attribute) WriterStereoOrder (cosmolkit.SmilesParseErrorKind attribute) WriterULong (cosmolkit.SmilesParseErrorKind attribute) WriterValence (cosmolkit.SmilesParseErrorKind attribute) WriteZero (cosmolkit.IoErrorKind attribute) WrongFormat (cosmolkit.BioReadErrorKind attribute) WrongGraphKind (cosmolkit.SdfErrorKind attribute) X XE (cosmolkit.Element attribute) XmlParseError XmlParseErrorKind (class in cosmolkit) XmlTextPos (class in cosmolkit) XorComposite (cosmolkit.SmartsWriteErrorKind attribute) XPE (cosmolkit.ResidueCode attribute) XYP (cosmolkit.ResidueCode attribute) XyzRead (cosmolkit.MolecularIoErrorKind attribute) XyzReadError XyzReadErrorKind (class in cosmolkit) XyzWrite (cosmolkit.MolecularIoErrorKind attribute) XyzWriteError XyzWriteErrorKind (class in cosmolkit) XyzWriteParams (class in cosmolkit) Y Y (cosmolkit.Element attribute) Y1 (cosmolkit.ResidueCode attribute) YB (cosmolkit.Element attribute) YCM (cosmolkit.ResidueCode attribute) yielded_count (cosmolkit.StereoisomerIterator attribute) YT3 (cosmolkit.ResidueCode attribute) Z Z (cosmolkit.BondStereo attribute) (cosmolkit.CipDescriptor attribute) z (cosmolkit.CipDescriptor attribute) (cosmolkit.CoordinateInputError property) z_pdb (cosmolkit.BioCrystalInfo attribute) z_policy (cosmolkit.Coordinate2DInputParams attribute) ZERO (cosmolkit.BondOrder attribute) Zero (cosmolkit.BondOrder attribute) ZERO_BONDS (cosmolkit.CxSmilesFields attribute) ZeroLengthVector (cosmolkit.StereoErrorKind attribute) ZeroSize (cosmolkit.TopologicalTorsionPathScoreErrorKind attribute) ZN (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) ZN2 (cosmolkit.ResidueCode attribute) ZR (cosmolkit.Element attribute)